[gmx-users] Generating a .gro file from .pdb file

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 12:53:27 CEST 2009

Lum Nforbi wrote:
> Hello everyone,
>   Thanks to Justin Lemkul and Thomas Schlesier for replying to my 
> question in vol. 65 issues 96 and 98.
>   I am trying to convert a pdb file to a gro file using pdb2gmx -f 
> waters.pdb -o waters.gro and I get the message:
> 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 don't want to use any of these force fields. I want to use the 
> charmm27 one. How do I select that? Do I need to modify the code? If so, 
> where do I find it?

I believe the CHARMM force fields are in the development version of the code 
(which you can get through git - see the website).  CHARMM will officially be 
supported in version 4.1, I believe.

>       Also, I read in a Spidertoxin tutorial that editconf can be used 
> to convert a .pdb file to a .gro file. I tried this but error message 
> says: "No velocities found." I know that pdb files generally do not have 
> velocities and these velocities can be generated by setting genvel=yes 
> in the mdp file. How can a .pdb file contain initial velocities?

That's not an error, really.  A .pdb file cannot, by virtue of its format, 
contain velocities.  You have it right that you need "gen_vel = yes" to get 
started, once you've reached grompp.


> Thank you,
> Lum
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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