[gmx-users] Selecting force field for simulation in vacuum

[Nuno Azoia]

Hello everyone!

I'm having some problems for selecting force field for a simulation in
vacuum. I'm using version 4.0.2.
According to pdb2gmx man page (pdb2gmx -h)

        DESCRIPTION
        -----------
        This program reads a pdb file, reads some database files, adds
        hydrogens to
        the molecules and generates coordinates in Gromacs (Gromos)
        format and a
        topology in Gromacs format. These files can subsequently be
        processed to
        generate a run input file. 
        
        The force fields in the distribution are currently:
        
        oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
        G43b1  GROMOS96 43b1 Vacuum Forcefield 
        G43a1  GROMOS96 43a1 Forcefield 
        G43a2  GROMOS96 43a2 Forcefield (improved alkane dihedrals)
        G45a3  GROMOS96 45a3 Forcefield 
        G53a5  GROMOS96 53a5 Forcefield 
        G53a6  GROMOS96 53a6 Forcefield 
        gmx    Gromacs Forcefield (a modified GROMOS87, see manual)
        encads Encad all-atom force field, using scaled-down vacuum
        charges
        encadv Encad all-atom force field, using full solvent charges


Ok. I would like to use G43b1, but when I run

pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n system.ndx -i
posre.itp  -inter -ignh

I just get this options, with no possibility for choosing G43b1:

        Select the Force Field:
         0: GROMOS96 43a1 force field 
         1: GROMOS96 43a2 force field (improved alkane dihedrals)
         2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
         3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 
         4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 
         5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
         6: [DEPRECATED] Gromacs force field (see manual)
         7: [DEPRECATED] Gromacs force field with hydrogens for NMR
         8: Encad all-atom force field, using scaled-down vacuum charges
         9: Encad all-atom force field, using full solvent charges    


I search on the mailing list for some solution and I get this message
from Berk Hess
(http://www.gromacs.org/component/option,com_wrapper/Itemid,165/)

        The GROMOS96 G43b1 "vacuum" force field has been removed.
        This confusing "vacuum" naming of this force field could make people
        think that this force field was optimized for real vacuum simulations,
        whereas it is actually G43a1 with neutralized charged residues.
        This force field has never been used seriously.

Now I'm confused! Ok, there is no more G43b1.
So I would like to ask witch force field I can use for simulations in vaccum? If I search on the mailing list I get the advice of using G43b1.
Can anyone help me on this.

And just another small thing. Maybe it would be good to remove the reference to G43b1 on the pdb2gmx man page.

Thank you in advance.

Nuno Azoia

--

Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Textil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt