Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error.
On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Biswajit Gorai wrote: >> >> Dear Bipin, >> Edit your topology file as: >> >> ########################################### >> ; Include forcefield parameters >> #include "amber99sb-ildn.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Ion_chain_A2.itp" >> >> *#include "oct.itp"* >> > > If oct.itp introduces new atom types (as the original .top does, for GAFF), > placing this topology here will result in a fatal error since there is a new > [atomtypes] directive that is introduced after the protein [moleculetype]. > If oct.itp does not introduce any new atom types, its location within the > system topology is irrelevant. > >> ; Include water topology >> #include "amber99sb-ildn.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber99sb-ildn.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Ion_chain_A2 1 >> *1-octanol 1 >> * >> *SOL 8987* > > > Depending on the order of the coordinate file, it may not be possible to > merge the SOL entries in this way. > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- ----------------------- Regards, Bipin Singh -- 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
