[gmx-users] pdb2gmx and virtual sites

Ondrej Marsalek ondrej.marsalek at gmail.com
Wed Nov 4 20:04:07 CET 2009

Dear GROMACS users,

I would like to substitute hydrogens in a protein with virtual sites
to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
several other places. So far, I have not found an example or a
tutorial that would involve this, so I want to create a
straightforward example. I have taken the 2KO3 structure from the PDB
and went through this sequence of commands:

pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
-vsite hydrogens -ignh
editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro

I also provided a pretty standard grompp.mdp, that contains
"constraints = h-angles". I get the following error:

Program grompp, VERSION 4.0.5
Source code file: vsite_parm.c, line: 779

Fatal error:
Automatic parameter generation not supported for Virtual site 3 atom 4
for this bonding configuration

I am not sure what the problem is. I would appreciate and help on the
use of this feature, pointers to resources, or a working example.
Reading the manual and searching did not help as much as I would like.


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