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

Lum Nforbi lumngwegia at gmail.com
Mon Sep 28 12:46:41 CEST 2009

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?

Thank you,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090928/c630bd47/attachment.html>

More information about the gromacs.org_gmx-users mailing list