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

Vitaly V. Chaban vvchaban at gmail.com
Mon Sep 28 15:04:38 CEST 2009


editconf -f waters.pdb -o conf.pdb

As for CHARMM, you may select the atoms of interest and incorporate to
your topology (see chapter 5 of the manual)
Also maybe some script for the conversion exist, try to search.


> 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?
>      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?

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