[gmx-users] Generating a .gro file from .pdb file
lumngwegia at gmail.com
Mon Sep 28 12:46:41 CEST 2009
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
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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