[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,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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