Dear Mark and Justin, Thank you for the clarification. Running the pdb2gmx with the following switches was enough to get a working topology file: pdb2gmx -v -f sys9-tmp.pdb -water spc -noter -o sys9-tmp.gro -p sys9-tmp.top -i sys9-tmp.itp -renum
The resulting topology file is very simple: ; Include forcefield parameters #include "./charmm36cgenff.ff/forcefield.itp" ; Include chain topologies #include "sys9-tmp-polymer.itp" ; Include Position restraint file for polymer #ifdef POSRES #include "sys9-tmp-polymer-pr.itp" #endif #include "sys9-tmp-lipid.itp" ; Include Position restraint file for lipids #ifdef POSRES #include "sys9-tmp-lipid-pr.itp" #endif ; Include water topology #include "./charmm36cgenff.ff/spc.itp" ; Include topology for ions #include "./charmm36cgenff.ff/ions.itp" [ system ] ; Name Polymer and lipid bilayer in water [ molecules ] ; Compound #mols POLYMER 1 LIPID 1 SOL 2295 CL 2 Thanks for the explanations for I understood that one needs to specify the exact number of molecules in the [ molecules ] section, though it seems that's not neccessarily the case as both Justin and Mark pointed out. I also noticed the unit cell size gets properly detected and written at the end of the GRO file. Best, Jernej -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
