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 grompp 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. Thanks, Ondrej _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
