1. DESCRIPCIÓ TEÒRICA DEL PROGRAMA


    Grumos és l'interfície per a poder executar el programa GROMOS; un programa dissenyat per a realitzar la simulació de la dinàmica molecular per a estudis de sistemes biomoleculars.

    Els objectius del programa, són:


    1. Predicció de la dependència de la conformació molecular amb l'entorn en el què es troba (aigua, etanol, cloroform, DMSO, solvent apolar, ...)
    2. Càlcul de les constants relatives d'enllaç tot evaluant diferències de l'energia lliure entre diversos complexos moleculars a partir d'integracions termodinàmiques, perturbacions i extrapolacions.
    3. Predicció de canvis energètics i estructurals causats per modificacionsd'aà en enzims o en parells de bases a l'ADN.
    4. Derivació en tres dimensions (3D) de l'estructura molecular basats en dades obtingudes a partir del NMR.
    5. Modelatge dinàmic de complexes moleculars
    6. Predicció de les propietats dels materials sota condicions extremes de temperatura i pressió, les quals poden ser experimentalment inaccessibles.




  2. DESCRIPCIÓ PRÀCTICA DELS COMANDAMENTS DEL PROGRAMA I EXEMPLES DE COMANDAMENTS I CONDICIONS APLICADES EN L´EXECUCIÓ


    Realitzarem la simulació de la Dinàmica Molecular sense solvent, només en el millor dels models: probl1amb3_2.ent (model2.pdb).


    Abans de correr el programa grumos, haurem de comprovar si aquesta estructura presenta residus de Cys prou aprop per a formar ponts disulfur.

    Aquesta comprovació la podem fer tot visualitzant l'estructura en Rasmol i assenyalant-ne tots els residus de Cys: 




    RasMol> pick distance
RasMol>
Atom #1: CYS175.SG (1286)
RasMol>
Atom #2: CYS53.SG (405)
Distance CYS175.SG-CYS53.SG: 16.227

    La distància entre el dos residus de Cys, és de 16.227Å, massa gran per a formar un pont disulfur.

    Una altra cosa que cal revisar abans d'executar el programa, és comprovar la terminació del model en l'arxiu .pdb en el cas que haguem modificat l'estructura (si per exemple li hem tret les cues).

    Ens hem d'assegurar que l'última fila de l'estructura presenti: 


    ATOM   2103  NH1 ARG   283      14.834   3.028  42.614  1.00198.16       1SG2104
ATOM   2104  NH2 ARG   283      16.193   1.104  42.428  1.00198.16       1SG2105
ATOM   2105  C   ARG   283      13.218   5.282  46.378  1.00198.16       1SG2106
ATOM   2106  O   ARG   283      14.115   6.046  46.732  1.00198.16       1SG2107
ATOM   2107  OXT ARG   283      12.720   5.305  45.134  1.00102.49       1SG2108
TER


    Un cop revisats el possibles ponts S-S, comprovada la terminació del .pdb, només cal realitzar la següent comanda per tal de solucionar algun possible problema de format existent en l'estructura del model (consisteix a passar un filtre al nostre .pdb):


    $ arrange.pl nommodel grumosnommodel.pdb


    L'execució d'aquest interactiu programa mostra les següents instruccions per pantalla, de les quals en resalto: 


    [e14910.bio.acexs.au.upf@au48239 practica_7]$ grumos



 This program prepares the drivers  to run GROMOS package
 You have to define the pathway in your directory
 A Protein Data Bank (PDB) file is needed here
 A generic name may be xxxx.pdb or whatever name you want
 The only thing you have to comply with is the format PDB
 Tell me path & file with the structure PDB  :

 NAME  >  /disc9/BE/e14910/practica_7/grumosmodel2.pdb
 You have to select the name of a directory where you want to work
 The default option is .../pro-grumos/

 Give me the directory name :     grumos-model2
mkdir: no se puede crear el directorio `grumos-model2': File exists


      P  R  O  -  G  R  U  M  O  S


  Program to run GROMOS package, made in the
  Institut de Biologia Fonamental (I.B.F.)
  Universidad Autonoma de Barcelona. Spain
            and
  Department of Physical Chemistry
   Uppsala University

  Version : 2.0



  Author: Baldomero Oliva  Nov.1990

  Revised and tested by :  O. TAPIA   Feb.1991

  Last revision: Baldomero Oliva  (Nov. 1993)



dl jun 2 10:13:32 CEST 2003



  At this point you may be interested in carrying out
  a free energy calculation, or/and dynamic run
  you must define now the files where the restraints are defined
  These files are necessary to run other inputs

  Do you need some more files?  yes/<no> : no


  Do  you want to clean the directory you gave me?  yes/<no> : yes

 Do you really want to clean that directory : grumos-model2 ?  yes/<no> : yes
 Now I am going to copy a set of driver names necessary to set up the run

cp /disc9/grumos93/interface/sh/driveropt_em /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to run the optimization


cp /disc9/grumos93/interface/sh/driveropt_emS /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to run the optimization of Complex Systems


cp /disc9/grumos93/interface/sh/driveropt_cem /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_cemS /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_cemw /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_cemi /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_cem /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_cemS /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_cemw /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_cemi /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_cem /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_top6 /disc9/BE/e14910/practica_7/grumos-model2

 This are the drivers & programs to continue the
 optimization



 This is the program to choose the size of the BOX in
 case you want to run a process with water molecules



 This is the program to change the inputs when the size
 of the BOX also change in case you want to run a process
 with water molecules, because then also it can be removed
 the radius of the boundaries and the radius to calculate
 the interaction on the potential


cp /disc9/grumos93/interface/sh/driveropt_emw /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to run the optimization of one system
 with water molecules


cp /disc9/grumos93/interface/sh/driveropt_emi /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to run the optimization of one system
 with water molecules plus ions



 This program reorganize the pdb file to run PROGROMOS



 This program reorganize the water molecules of the
 crystal as solvent molecules


cp /disc9/grumos93/interface/sh/exedriveropt_em /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to execute the optimization of the
 system without water molecules and solvent simulated


cp /disc9/grumos93/interface/sh/exedriveropt_emS /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to execute the optimization of the
 Complex Systems


cp /disc9/grumos93/interface/sh/exedriveropt_emw /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to execute driveropt_emw


cp /disc9/grumos93/interface/sh/exedriveropt_emi /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to execute driveropt_emi


  I am sorry but I have to continue preparing all the drivers you will need


cp /disc9/grumos93/interface/sh/menu_grumos    /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/menu_return /disc9/BE/e14910/practica_7/grumos-model2

 This is the MENU of GRUMOS


cp /disc9/grumos93/interface/sh/menu_analyses /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/menu_returan /disc9/BE/e14910/practica_7/grumos-model2

 This is the MENU for the analyses


cp /disc9/grumos93/interface/sh/driver_top3 /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_top5 /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_merge /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_reducmt /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_rmt /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_reducmt /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_patch /disc9/BE/e14910/practica_7/grumos-model2
/.driver_patch
cp /disc9/grumos93/interface/sh/exedriver_patch /disc9/BE/e14910/practica_7/grumos-model2
/.exedriver_patch
cp /disc9/grumos93/interface/sh/driver_unpatch /disc9/BE/e14910/practica_7/grumos-model2
/.driver_unpatch
cp /disc9/grumos93/interface/sh/exedriver_unpatch /disc9/BE/e14910/practica_7/grumos-model2
/.exedriver_unpatch

 This are the drivers to run the topology of the system

cp /disc9/grumos93/interface/sh/driver_md2 /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_mdS /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_md2 /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_mdS /disc9/BE/e14910/practica_7/grumos-model2

 This is the driver to run the DYNAMIC


cp /disc9/grumos93/interface/sh/driveropt_water /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_water /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_mergewater /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_mergeion /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_ion /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_ion /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_water /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_mergewater /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_mergeion /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_ion /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_water_untop /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driveropt_ion_untop /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_water_untop /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriveropt_ion_untop /disc9/BE/e14910/practica_7/grumos-model2

 This are the drivers to add the water molecules and
 the ions,  and also to optimize the new coordinates
 of the system

cp /disc9/grumos93/interface/sh/driver_cmd /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/driver_cmdS /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_cmd /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/sh/exedriver_cmdS /disc9/BE/e14910/practica_7/grumos-model2

 This are the drivers to continue the dynamic

cp /disc9/grumos93/interface/dat/cebador_em /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/exe/cont_md /disc9/BE/e14910/practica_7/grumos-model2
cp: no se puede abrir `/disc9/grumos93/interface/exe/cont_md' para lectura: Permission denied
cp /disc9/grumos93/interface/sh/cont_md2.f /disc9/BE/e14910/practica_7/grumos-model2

 This are the drivers to make the loop to run the
 dynamic and also the optimization

  I am preparing all the drivers you will need

cp /disc9/grumos93/interface/sh/changps /disc9/BE/e14910/practica_7/grumos-model2


 This are the programs to make the input of the DYNAMIC

  I am preparing all the drivers you will need






 This are the programs to make the input of the TOPOLOGY

  I am preparing all the drivers you will need



 This are the programs to make the input of the OPTIMIZATION


 This are the the programs to chose the radius of cut-off
 when there are water molecules in our system

  I am preparing all the drivers you will need

cp /disc9/grumos93/interface/dat/nada /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/dat/dict37.dat /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/dat/dic37d.dat /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/dat/merge_top.dat /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/dat/make_box.dat /disc9/BE/e14910/practica_7/grumos-model2
cp /disc9/grumos93/interface/dat/spc216.dat /disc9/BE/e14910/practica_7/grumos-model2

 This are the data files for the analyses and the
 dynamic with water molecules.
 The file WATER-EM.DAT_OLD can be fixed to make the
 optimization of the waters and ions when surrounding
 the protein.

   DRIVERS AND PROGRAMS FOR THE ANALYSIS







cp /disc9/grumos93/interface/sh/exedriver_avx /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_avx /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_transform /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_transform /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_ajc /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_ajc /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_ahb /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_ahb /disc9/BE/e14910/practica_7/grumos-model2




cp /disc9/grumos93/interface/sh/exedriver_rms /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_rms /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_momentum /disc9/BE/e14910/practica_7/grumos-model2


cp /disc9/grumos93/interface/sh/driver_momentum /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_imsdm /disc9/BE/e14910/practica_7/grumos-model2


cp /disc9/grumos93/interface/sh/driver_imsdm /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/exedriver_lsq /disc9/BE/e14910/practica_7/grumos-model2

cp /disc9/grumos93/interface/sh/driver_lsq /disc9/BE/e14910/practica_7/grumos-model2




cp /disc9/grumos93/interface/sh/exedriver_comp /disc9/BE/e14910/practica_7/grumos-model2


     R U N N I N G  the  P R O G R A M


 Now you are invited to answer the questions of the menu_grumos



     THERE IS NOT A TERMINAL IDENTIFICATION
               IN YOUR DATA FILE

  Check if the program runs, if it is not then follow
  the next instructions.

  You must include the finalization before to run
  this program.

  Write the oxygen terminal of the protein if it is not.
  Include as a new line the same last one,substituting
  the remark ATOM by TER in your PDB file and restart
  the process again .



 Options :

 <a> =====> Continue

  b  =====> Break

   a


 Options :



<a> ====>  Create INPUTS


 b  ====>  RUN a process


 c  ====>  ANALYSIS


 d  ====>  NEW SIMULATION


 e  ====>  Logout of this program



 a

 Options of INPUT  :



<a> ====> TOPOLOGY


 b  ====> ENERGY OPTIMIZATION


 c  ====> DYNAMIC


 d  ====> Go to MENU



 a



 Options :


<a> =====>   Single System


 b  =====>   Complex System


 c  =====>   Reduce and obtain the formatted topology


 d  =====>   Modify topology


 e  =====>   Go to MENU



 a



                T O P O L O G Y



   This program read the PDB file. Then, it decides
   if there are disulphide bridges by reading the number
   of SSBOND with the residue CYS ( and not other!
   e.g. CYSH ),it creates a GSF file (old WVG files)
   and the input to run PROGMT.

   The file PDB will be previously rebuilt, in order
   to make the correct numbering of the residues, and
   recalled as :      NAME-OF-PROTEIN.pdbINP

   It will be possible to change the name of the resi-
   dues, but the PDB file will go on having the same
   residue, that means that the only possibility for
   changes will be between names which belong to the
   same residue, for instance :

   1) HISA can be changed into HISB
   2) CYS can be changed into CYS1 or CYS2
   3) GLU and ASP can be changed by GLUH and ASPH
   etc.

   It will be possible also to remove the prostetic
   groups or other groups which apear in  the crystal,
   as for exemple water molecules and counter ions, and
   these also will be removed when to make the GSF file

   One title will be chosen to define all the stuff in
   this directory. It would be interesting for your
   own profit to write on it the name of the molecule,
   the principal characteristic of the simulation, as
   for instance the use or not of solvent, the radius
   of cut-off and cut-on, the charge in the tails N
   and C terminal, etc., and finally the date of the
   work, but just remind that the title can not be
   longer than 80 characters.

   Finally it will be possible to choose between a si-
   mulation with water molecules as solvent or with the
   so called NIS ( non inertial solvent) model,and also
   will be possible to choose the chemical state of the
   tails depending on the pH.

   In case the simulation with water molecules was selec-
   ted, it will be also possible to choose the ionic
   stength, and this will be obtained by adding sodium
   cloride ions. Depending in the tolerance of the error
   to get the ionic strength it will be made the BOX
   which hold the system, that means , if the tolerance
   is very small then the BOX will increase at the same
   time than the number of ions until the correct point
   will be reached.





                 T I T L E
grumosmodel2

   Name of PDB file :  grumosmodel2.pdb
                 Aminoacid(  1):  GLY
                 Aminoacid(  2):  ILE
                 Aminoacid(  3):  LYSH
                 Aminoacid(  4):  VAL
                 Aminoacid(  5):  ILE
                 Aminoacid(  6):  LYSH
                 Aminoacid(  7):  ALA
                 Aminoacid(  8):  PRO
                 Aminoacid(  9):  GLU
                 Aminoacid( 10):  MET
                 Aminoacid( 11):  TRP
                 Aminoacid( 12):  ALA
                 Aminoacid( 13):  LYSH
                 Aminoacid( 14):  GLY
                 Aminoacid( 15):  VAL
                 Aminoacid( 16):  LYSH
                 Aminoacid( 17):  GLY
                 Aminoacid( 18):  LYSH
                 Aminoacid( 19):  ASN
                 Aminoacid( 20):  ILE
                 Aminoacid( 21):  LYSH
                 Aminoacid( 22):  VAL
                 Aminoacid( 23):  ALA
                 Aminoacid( 24):  VAL
                 Aminoacid( 25):  LEU
                 Aminoacid( 26):  ASP
                 Aminoacid( 27):  THR
                 Aminoacid( 28):  GLY
                 Aminoacid( 29):  CYSH
                 Aminoacid( 30):  ASP
                 Aminoacid( 31):  THR
                 Aminoacid( 32):  SER
                 Aminoacid( 33):  HISA
                 Aminoacid( 34):  PRO
                 Aminoacid( 35):  ASP
                 Aminoacid( 36):  LEU
                 Aminoacid( 37):  LYSH
                 Aminoacid( 38):  ASN
                 Aminoacid( 39):  GLN
                 Aminoacid( 40):  ILE
                 Aminoacid( 41):  ILE
                 Aminoacid( 42):  GLY
                 Aminoacid( 43):  GLY
                 Aminoacid( 44):  LYSH
                 Aminoacid( 45):  ASN
                 Aminoacid( 46):  PHE
                 Aminoacid( 47):  THR
                 Aminoacid( 48):  ASP
                 Aminoacid( 49):  ASP
                 Aminoacid( 50):  ASP
                 Aminoacid( 51):  GLY
                 Aminoacid( 52):  GLY
                 Aminoacid( 53):  LYSH
                 Aminoacid( 54):  GLU
                 Aminoacid( 55):  ASP
                 Aminoacid( 56):  ALA
                 Aminoacid( 57):  ILE
                 Aminoacid( 58):  SER
                 Aminoacid( 59):  ASP
                 Aminoacid( 60):  TYR
                 Aminoacid( 61):  ASN
                 Aminoacid( 62):  GLY
                 Aminoacid( 63):  HISA
                 Aminoacid( 64):  GLY
                 Aminoacid( 65):  THR
                 Aminoacid( 66):  HISA
                 Aminoacid( 67):  VAL
                 Aminoacid( 68):  ALA
                 Aminoacid( 69):  GLY
                 Aminoacid( 70):  THR
                 Aminoacid( 71):  ILE
                 Aminoacid( 72):  ALA
                 Aminoacid( 73):  ALA
                 Aminoacid( 74):  ASN
                 Aminoacid( 75):  ASP
                 Aminoacid( 76):  SER
                 Aminoacid( 77):  ASN
                 Aminoacid( 78):  GLY
                 Aminoacid( 79):  GLY
                 Aminoacid( 80):  ILE
                 Aminoacid( 81):  ALA
                 Aminoacid( 82):  GLY
                 Aminoacid( 83):  VAL
                 Aminoacid( 84):  ALA
                 Aminoacid( 85):  PRO
                 Aminoacid( 86):  GLU
                 Aminoacid( 87):  ALA
                 Aminoacid( 88):  SER
                 Aminoacid( 89):  LEU
                 Aminoacid( 90):  LEU
                 Aminoacid( 91):  ILE
                 Aminoacid( 92):  VAL
                 Aminoacid( 93):  LYSH
                 Aminoacid( 94):  VAL
                 Aminoacid( 95):  LEU
                 Aminoacid( 96):  GLY
                 Aminoacid( 97):  GLY
                 Aminoacid( 98):  GLU
                 Aminoacid( 99):  ASN
                 Aminoacid(100):  GLY
                 Aminoacid(101):  SER
                 Aminoacid(102):  GLY
                 Aminoacid(103):  GLN
                 Aminoacid(104):  TYR
                 Aminoacid(105):  GLU
                 Aminoacid(106):  TRP
                 Aminoacid(107):  ILE
                 Aminoacid(108):  ILE
                 Aminoacid(109):  ASN
                 Aminoacid(110):  GLY
                 Aminoacid(111):  ILE
                 Aminoacid(112):  ASN
                 Aminoacid(113):  TYR
                 Aminoacid(114):  ALA
                 Aminoacid(115):  VAL
                 Aminoacid(116):  GLU
                 Aminoacid(117):  GLN
                 Aminoacid(118):  LYSH
                 Aminoacid(119):  VAL
                 Aminoacid(120):  ASP
                 Aminoacid(121):  ILE
                 Aminoacid(122):  ILE
                 Aminoacid(123):  SER
                 Aminoacid(124):  MET
                 Aminoacid(125):  SER
                 Aminoacid(126):  LEU
                 Aminoacid(127):  GLY
                 Aminoacid(128):  GLY
                 Aminoacid(129):  PRO
                 Aminoacid(130):  SER
                 Aminoacid(131):  ASP
                 Aminoacid(132):  VAL
                 Aminoacid(133):  PRO
                 Aminoacid(134):  GLU
                 Aminoacid(135):  LEU
                 Aminoacid(136):  LYSH
                 Aminoacid(137):  GLU
                 Aminoacid(138):  ALA
                 Aminoacid(139):  VAL
                 Aminoacid(140):  LYSH
                 Aminoacid(141):  ASN
                 Aminoacid(142):  ALA
                 Aminoacid(143):  VAL
                 Aminoacid(144):  LYSH
                 Aminoacid(145):  ASN
                 Aminoacid(146):  GLY
                 Aminoacid(147):  VAL
                 Aminoacid(148):  LEU
                 Aminoacid(149):  VAL
                 Aminoacid(150):  VAL
                 Aminoacid(151):  CYSH
                 Aminoacid(152):  ALA
                 Aminoacid(153):  ALA
                 Aminoacid(154):  GLY
                 Aminoacid(155):  ASN
                 Aminoacid(156):  GLU
                 Aminoacid(157):  GLY
                 Aminoacid(158):  ASP
                 Aminoacid(159):  GLY
                 Aminoacid(160):  ASP
                 Aminoacid(161):  GLU
                 Aminoacid(162):  ARG
                 Aminoacid(163):  THR
                 Aminoacid(164):  GLU
                 Aminoacid(165):  GLU
                 Aminoacid(166):  LEU
                 Aminoacid(167):  SER
                 Aminoacid(168):  TYR
                 Aminoacid(169):  PRO
                 Aminoacid(170):  ALA
                 Aminoacid(171):  ALA
                 Aminoacid(172):  TYR
                 Aminoacid(173):  ASN
                 Aminoacid(174):  GLU
                 Aminoacid(175):  VAL
                 Aminoacid(176):  ILE
                 Aminoacid(177):  ALA
                 Aminoacid(178):  VAL
                 Aminoacid(179):  GLY
                 Aminoacid(180):  SER
                 Aminoacid(181):  VAL
                 Aminoacid(182):  SER
                 Aminoacid(183):  VAL
                 Aminoacid(184):  ALA
                 Aminoacid(185):  ARG
                 Aminoacid(186):  GLU
                 Aminoacid(187):  LEU
                 Aminoacid(188):  SER
                 Aminoacid(189):  GLU
                 Aminoacid(190):  PHE
                 Aminoacid(191):  SER
                 Aminoacid(192):  ASN
                 Aminoacid(193):  ALA
                 Aminoacid(194):  ASN
                 Aminoacid(195):  LYSH
                 Aminoacid(196):  GLU
                 Aminoacid(197):  ILE
                 Aminoacid(198):  ASP
                 Aminoacid(199):  LEU
                 Aminoacid(200):  VAL
                 Aminoacid(201):  ALA
                 Aminoacid(202):  PRO
                 Aminoacid(203):  GLY
                 Aminoacid(204):  GLU
                 Aminoacid(205):  ASN
                 Aminoacid(206):  ILE
                 Aminoacid(207):  LEU
                 Aminoacid(208):  SER
                 Aminoacid(209):  THR
                 Aminoacid(210):  LEU
                 Aminoacid(211):  PRO
                 Aminoacid(212):  ASN
                 Aminoacid(213):  LYSH
                 Aminoacid(214):  LYSH
                 Aminoacid(215):  TYR
                 Aminoacid(216):  GLY
                 Aminoacid(217):  LYSH
                 Aminoacid(218):  LEU
                 Aminoacid(219):  THR
                 Aminoacid(220):  GLY
                 Aminoacid(221):  THR
                 Aminoacid(222):  SER
                 Aminoacid(223):  MET
                 Aminoacid(224):  ALA
                 Aminoacid(225):  ALA
                 Aminoacid(226):  PRO
                 Aminoacid(227):  HISA
                 Aminoacid(228):  VAL
                 Aminoacid(229):  SER
                 Aminoacid(230):  GLY
                 Aminoacid(231):  ALA
                 Aminoacid(232):  LEU
                 Aminoacid(233):  ALA
                 Aminoacid(234):  LEU
                 Aminoacid(235):  ILE
                 Aminoacid(236):  LYSH
                 Aminoacid(237):  SER
                 Aminoacid(238):  TYR
                 Aminoacid(239):  GLU
                 Aminoacid(240):  GLU
                 Aminoacid(241):  GLU
                 Aminoacid(242):  SER
                 Aminoacid(243):  PHE
                 Aminoacid(244):  GLN
                 Aminoacid(245):  ARG
                 Aminoacid(246):  LYSH
                 Aminoacid(247):  LEU
                 Aminoacid(248):  SER
                 Aminoacid(249):  GLU
                 Aminoacid(250):  SER
                 Aminoacid(251):  GLU
                 Aminoacid(252):  VAL
                 Aminoacid(253):  PHE
                 Aminoacid(254):  ALA
                 Aminoacid(255):  GLN
                 Aminoacid(256):  LEU
                 Aminoacid(257):  ILE
                 Aminoacid(258):  ARG
                 Aminoacid(259):  ARG

   Number of aA in the chain:    259

   Do you want change the name of some residue,         YES/<NO> : NO





  CYS residues list :

   Residue CYS :    29
   Residue CYS :   151

  You must call CYS1-CYS2 the residues with the bond

   Are there disulphide bridges? YES/<NO> :   NO


   Do you want change the name of some residue,         YES/<NO> : NO





   Options
                <1>  Non inertial solvent, NIS model
                 2   Explicit WATER SPC simulation
                 3   Explicit WATER SPC/E simulation
                 4   Charged Force Field in vacuum
   Value:  1


   Options
                <1>  Head NH3 and Tail COO  ==>  6 ( pH )  8
                 2   Head NH3 and Tail COOH ==>  0 ( pH )  2
                 3   Head NH2 and Tail COO  ==> 12 ( pH ) 14
                 4   Head NH2 and Tail COOH ==> Specific cases
   Value:  1








 Options :



<a> ====>  Create INPUTS


 b  ====>  RUN a process


 c  ====>  ANALYSIS


 d  ====>  NEW SIMULATION


 e  ====>  Logout of this program



 b

 Options to RUN :



 <a> ====> TOPOLOGY


  b  ====> ENERGY OPTIMIZATION


  c  ====> DYNAMIC


  d  ====> Go to MENU



 a



 Options :


<a>   =====>   Single System


 b    =====>   Complex System


 c    =====>   Reduce and obtain the formatted topology


 d    =====>   Modify topology


 e    =====>   Transform formated to binary topology


 f    =====>   Modify the water BOX


 g    =====>   Add water molecules to the optimized solute


 h    =====>   Add counter ions to the solvated solute


 i    =====>   Go to MENU



 a



 Directory where is the work :  
 /disc9/BE/e14910/practica_7/grumos-model2


 Running the topology without ions

rm: no se puede borrar `fort.10': No such file or directory
rm: no se puede borrar `fort.11': No such file or directory
rm: no se puede borrar `fort.12': No such file or directory
rm: no se puede borrar `fort.9': No such file or directory


 ERRORS IN THE OUTPUT OF PRUGMT :

 LAST 5  LINES OF PRUGMT-OUTPUT



 NAEX14: 4069


     NATOM     NCAG     NAEX  NAEX1-4    NBONH     NBON    NTHEH     NTHE
      2403     1464     6332     4069      491     1939      912     2623

      NQHIH     NQHI    NPHIH     NPHI     NRPD     NRPA
       400      765       91     1230        0        0

 The topology is ready


 Including polar Hydrogens



   491 HYDROGEN ATOMS WILL BE GENERATED


 ERRORS IN THE OUTPUT OF PRUGCH :


 LAST 5  LINES OF PRUGCH-OUTPUT




 3.  A T O M   C O O R D I N A T E S   :


 grumosmodel2


 Options :



<a> ====>  Create INPUTS


 b  ====>  RUN a process


 c  ====>  ANALYSIS


 d  ====>  NEW SIMULATION


 e  ====>  Logout of this program

 
 a


 Options of INPUT  :



<a> ====> TOPOLOGY


 b  ====> ENERGY OPTIMIZATION


 c  ====> DYNAMIC


 d  ====> Go to MENU



 b

 Have you run the TOPOLOGY program ? no/<yes> yes



 Options :


<a>   =====>   Single System


 b    =====>   Complex System



 a


               O P T I M I Z A T I O N


   The optimization can be done by one of three
   different geometry methods :

      Steepest Descent

      Conjugate Gradient

      Both methods used alternatively


   The program PROEM will be run several times, and
   also this will be chosen.

   Each run involve several steps, and each step
   involves a value called LAMBDA to obtain a new
   set of coordinates. It will be necessary to define
   the maximum value of LAMBDA and the first value to
   start the optimization.

   The number of steps geting a new set of coordinates
   will be also chosen for each run.

   In case the method of Conjugate Gradient was chosen,
   it will be necessary to especify how many times the
   energy gradient in the step must be modified



   Options
                <1>   Conjugate Gradient & Steepest Descent
                 2    Steepest Descent
                 3    Conjugate Gradient

   Value:  2


   Number of steps in each run: 1000


   How many times the optimization must be run?       : 10

   First value of Lambda (parameter)  <0.05> :

   Maximum value of Lambda (parameter)<0.10> :



   Select now SHAKE options

   If you use SHAKE we suggest you to select
   bond-stretchings only. Bond angle and
   dihedrals are usually left free. OPTIONS:

   NO SHAKE

   Only the bonds which involve hydrogen atoms
   will be constrained :

   Constraints in IBH-JBH

   All the bonds are constrained

  (SHAKE) In addition IB-JB



   Finally is is also possible to choose if the
   bonds are constrained to the distance in the
   first set of coordinates :

   Length  =   CONSTR

   Or by the distance defined by the TOPOLOGY :

   Length  =   BO



   Options
      <1> SHAKE is not used
       2 Constraints from IBH-JBH,length=BO
       3 Constraints from IBH-JBH,length from CONSTR
       4 In adition from IB-JB,length=BO
       5 In adition from IB-JB,length from CONSTR

   Value :  1





   The calcul of the electric energy and
   Van der Waals energy can be made by three
   different methods :


   By scanning, which means that each step
   is calculated all the possible interactions
   between atoms pairs inside a further especified
   radius.


   By interaction of previous selected atoms pairs
   inside a further especified radius.   In this
   case it will be necessary to make a list of the
   atoms inside such a distance,  this list will
   be made by the same program,  but after several
   steps it will change. The program will ask for
   the number of steps to do it.



   By interaction of previous selected groups pairs
   inside a further especified radius.    In this
   case will be necessary to make a list of the
   atoms inside such a distance,  this list will
   be made by the same program,  but after several
   steps it will change. The program will ask for
   the number of steps to do it. And the groups are
   already defined by the topology program.



  Options
   <1> By interaction between groups pair
    2  By interaction between atoms pair
    3  By scanning
    4  By grid cells

   Value :  1

   After how many steps the list change <10> :


   The program will ask now for the radius value
   of cut-off & cut-on, RCUTL>RCUTP, as though
   as the radius values for the switching function.

   You can see :

     Effects of Truncating Long Range Forces on
     Protein Dynamics

     Loncharich ,R.J. &  Brooks ,B.R.

     Division of Computer Research & Technology
     National Institutes of Health (Bethesda)

     PROTEINS (1989) 6 , pp 32-45


   or


     Cut-off size does strongly influence Molecular
     Dynamics results on solvated polypeptides

     Schreiber,H.  &  Steinhauser, O.

     BIOCHEMISTRY (1991) 31 , pp 5856-5860



   Value of RCUTP <0.8 nm> :

   Value of RSWI2 <10.0 nm> :

   Value of RCUI2 <10.0 nm> :

   Value of RCUTL <1.3 nm> :



   Sequence radius to calculate the interaction: 99999




   At this point it will be possible to choose
   the shape and also the size of the BOX.

   Inside of this BOX the protein and molecules
   surrounding  will remain defined using the
   BOUNDARY CONDITIONS algorithm .



   Options
                <1>  No periodicity is taked into account
                 2   Octahedric BOX,BETA=90
                 3   Rombohedric BOX, chose BETA

   Value :  1




  At this point the program will ask for the different
  constraints.

  It will be necessary to especify the name of the file
  which has the atoms to restrain. In that case these
  must have been alocated in the working directory either
  from the beginning or before you run the program.

  The next questions will be related with the strength
  of the constraints and the distance between atoms,
  and to understand this questions read the
  GROMOS manual before.



  Options
   <1>  No position restraining
    2  Position restraining using CHO
    3  Idem using CHO/atomic B-factors
    Value :  1


  Options
   <1>  No distance restraining
    2  Distance restraining using CDIS
    3  Idem using CDIS*weight factors
    Value :  1

  Options
   <1>  No dihedral restraining
    2  Restraining using CDLR*weight factors
    Value :  1


   Print energy every n-steps, n=: 100



 Options:



<a> ====>  Create INPUTS


 b  ====>  RUN a process


 c  ====>  ANALYSIS


 d  ====>  NEW SIMULATION


 e  ====>  Logout of this program



 b

 Options to RUN:



 <a> ====> TOPOLOGY


  b  ====> ENERGY OPTIMIZATION


  c  ====> DYNAMIC


  d  ====> Go to MENU



 b




 Options:


<a> ====>       Single System


 b  ====>       Complex System



 a


 Have you run the TOPOLOGY program ? no/<yes> yes

 Have you made the DYNAMIC input ? no/<yes> no

 In this case you will have some errors, but the
 the program will run perfectly well.

 IF YOU ARE RUNNING A SYSTEM WITH WATER
 AS SOLVENT YOU WILL HAVE PROBLEMS

    BUILD THE DYNAMICS INPUT FIRST


 Do you want continue with the optimization ? no/<yes> yes

 Options  :

 <a> ====> Start the optimization

  b  ====> Continue the optimization

  c  ====> Optimize the water box

  d  ====> Optimize the counter-ions

  e  ====> Go to menu


  a



 Directory where is the work :  /disc9/BE/e14910/practica_7/grumos-model2


 Running a NIS simulation .
 You will found the information about errors in file.err

cp: no se puede efectuar `stat' sobre `.grumosmodel2_md.dat_old': No such file or directory
cp: no se puede efectuar `stat' sobre `.grumosmodel2_md.cdat_old': No such file or directory


 Options :



<a> ====>  Create INPUTS


 b  ====>  RUN a process


 c  ====>  ANALYSIS


 d  ====>  NEW SIMULATION


 e  ====>  Logout of this program



 e


    Com hem pogut veure en el transcurs de l´execuxció del programa, els passos que hem seguit:


    1. Crear inputs per després córrer Topology.
    2. Córrer Topology amb les condicions: sistema simple, sense ponts S-S, sense solvent inert, amb cues als extrems (NH3 i COO-).
    3. Crear inputs per a després córrer Energy Optimitzation.
    4. Córrer Energy Optimitzation amb les condicions: sistema simple, steepest descent (descens cap al mínim de forma molt pronunciada), correrem el programa 10 cops en 1000 passos i n´imprimirem els valors cada 100 resultats, sense constricció dels àtoms (només contempla la constricció dels àtoms d´H), interacció entre grups de parells, sense periodicitat i sense optimització per diedres...




  3. RESULTATS OBTINGUTS DE L´APLICACIÓ DEL PROGRAMA ALS EXEMPLES COMENTATS I PROBLEMES PROPOSATS A LA PRÀCTICA


    Els resultats obtinguts per al grumosmodel2.pdb, han estat els següents: 


    
[e14910.bio.acexs.au.upf@au491 practica_7]$ cd grumos-model2
[e14910.bio.acexs.au.upf@au491 grumos-model2]$ ls
total 3048
   4 coordinates/     336 grumosmodel2_top.bin         20 outgrumosmodel2_emnum004.lis 
   4 energies/         92 grumosmodel2.wvg             20 outgrumosmodel2_emnum005.lis   
   4 file.err         132 inicial.gsf                  20 outgrumosmodel2_emnum006.lis    
   4 file.errpdb       24 outgrumosmodel2_emnum001.lis 20 outgrumosmodel2_emnum007.lis
 132 grumosmodel2.hwvg 20 outgrumosmodel2_emnum002.lis 20 outgrumosmodel2_emnum008.lis
 108 grumosmodel2.pdb  20 outgrumosmodel2_emnum003.lis 20 outgrumosmodel2_emnum009.lis
	               20 outgrumosmodel2_emnum010.lis 2024 outgrumosmodel2_top.lis	
							4 outgrumosmodel2_h.lis
[e14910.bio.acexs.au.upf@au491 grumos-model2]$


    El que ens interessa observar d'aquests arxius de sortida, és si realment l'energia del sistema original ha disminuit (l'estructura s'ha relaxat i es troba en una conformació més estable).

    Per a comprovar-ho cal observar el primer dels outputs generats (outgrumosmodel2_emnum001.lis) i l'últim (outgrumosmodel2_emnum010.lis), i comprovar si el valor de l'energia potencial total ha passat d'un valor positiu a un valor negatiu: 


    3.  A T O M I C   C O O R D I N A T E S   :


 grumosmodel2
 Subrutina runem
 SHAKE COORDINATES, NITER =   1
 Subrutina Force

 NUMBER OF NON-BONDED CHARGE GROUP PAIRS (I>J) =  49518

 NJNB= 49518NTN= 2


 STEP NIP1 NIS1 NIP2 NIS2 NIP3 NIS3 NITI  STEP-SIZE [...] 
      E-POT-TOT   E-BOND-H     E-BOND  E-ANGLE-H  [...]       
    E-EL-G1-G1 E-EL-G1-G2 E-EL-G2-G2 E-EL-G1-G3 E-EL-G2-G3 E-EL-G3-G3 E-EL-G1-G4 [...]
   E-LJ-G1-G1 E-LJ-G1-G2 E-LJ-G2-G2 E-LJ-G1-G3 E-LJ-G2-G3 E-LJ-G3-G3 E-LJ-G1-G4 [...]
 E-DIS-R.   E-POS-R.   E-DIH-R.


      0    1    0    0    0    0    0    0 0.5000E-01 [...]
     0.13951E+05 0.1534E+02 0.1812E+04 0.4809E+03 [...] 
   -0.4697E+04 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 [...]
   0.3951E+04 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 [...]
  0.0000E+00 0.0000E+00 0.6815-269
  
  								
								

    [...]
    
							
							
STEP NIP1 NIS1 NIP2 NIS2 NIP3 NIS3 NITI  STEP-SIZE [...]
      E-POT-TOT   E-BOND-H     E-BOND  E-ANGLE-H    [...]   
    E-EL-G1-G1 E-EL-G1-G2 E-EL-G2-G2 E-EL-G1-G3 E-EL-G2-G3 E-EL-G3-G3 E-EL-G1-G4 [...]
   E-LJ-G1-G1 E-LJ-G1-G2 E-LJ-G2-G2 E-LJ-G1-G3 E-LJ-G2-G3 E-LJ-G3-G3 E-LJ-G1-G4 [...]
    E-DIS-R.   E-POS-R.   E-DIH-R.


  1000    1    0    0    0    0    0    0 0.3273E-03 [...]
   -0.15142E+05 0.1990E+02 0.1859E+03 0.1911E+03 [...] 
   -0.8314E+04 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 [...]
  -0.9897E+04 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 [...]
  0.0000E+00 0.0000E+00 0.6815-269

    ... i ara visualitzem els arxius continguts en el directori coordinates: 


    [e14910.bio.acexs.au.upf@au491 grumos-model2]$ cd coordinates/
[e14910.bio.acexs.au.upf@au491 coordinates]$ ls
total 5672
   4 anglen.log                  112 grumosmodel2xemnum006.gsf	     160 modelopt2.out       
   4 bplot.log                   112 grumosmodel2xemnum007.gsf       196 modelopt2.pdb
   4 clean.log                   112 grumosmodel2xemnum008.gsf	      28 modelopt2.pln
 108 grumosmodel2.pdb            112 grumosmodel2xemnum009.gsf	      36 modelopt2.rin
 112 grumosmodel2xemnum001.gsf   112 grumosmodel2xemnum010.gsf         4 modelopt2.sco
 112 grumosmodel2xemnum002.gsf   112 grumosmodel2xvmd0000.gsf         28 modelopt2.sdh
 112 grumosmodel2xemnum003.gsf   112 modelopt2.lan                    32 nb.log
 112 grumosmodel2xemnum004.gsf    76 modelopt2.nb		       4 pplot.log
 112 grumosmodel2xemnum005.gsf   180 modelopt2.new		       4 secstr.log
								       4 tplot.log
[e14910.bio.acexs.au.upf@au491 coordinates]$


    Per tal de comparar el meu model i el model optimitzat, correré el programa XAM de superposició estructural. Els arxius d'entrada per al programa són: grumosmodel2.pdb i grumosmodel2xvmd0010.gsf.


    La sortida del programa genera els següents arxius de sortida:

    1. un valor de RMSD (xammodelsgrumos2)
    2. una estructura (xammodelsgrumos2.pdb)


    Com es pot observar a partir de la imatge de les dues estructures superposades, ambdós models són força similars excepte en les regions dels loops: un cop més dir que aquestes regions són força variables.

    I finalment per a veure com de millor és el model optimitzat respecte l'original, correrem la comanda de procheck:


    Summary Summary


    Tot i que en fer el procheck el model optimitzat hauria de sortir millor, en aquest cas no ha estat així. De totes maneres el model optimitzat té una energia menor que l'original (com a resultat de l'optimització) i per tant em de creure que és un model millorat.