Hi Justin, thank you very much for your help!! > > > On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> thank you for your answer. >> >> Now I tried it with two different restraint .itp files. One for the >> protein and one for the dummy atoms. >> But still it doesn't work. Now the error is: >> >> [ file posre_memb.itp, line 5 ]: >> Atom index (4942) in position_restraints out of bounds (1-1). >> This probably means that you have inserted topology section >> "position_restraints" >> in a part belonging to a different molecule than you intended to. >> In that case move the "position_restraints" section to the right >> molecule. >> >> >> But I think I included it the right way: >> >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "amber03.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 "amber03.ff/ions.itp" >> >> #include "amber03.ff/dum.itp" >> #ifdef POSRES >> #include "posre_memb.itp" >> #endif >> >> >> >> In my coordiate file the difference between them look like this: >> >> 313LEU HD23 4938 3.813 4.505 3.308 >> 313LEU C 4939 3.435 4.335 3.190 >> 313LEU OC1 4940 3.429 4.330 3.090 >> 313LEU OC2 4941 3.337 4.305 3.259 >> 314DUM DUM 4942 1.996 2.371 6.171 >> 314DUM DUM 4943 1.996 2.371 6.271 >> 314DUM DUM 4944 1.996 2.471 6.171 >> 314DUM DUM 4945 1.996 2.471 6.271 >> >> >> my restraint file for the protein looks like this: >> >> >> ; position restraints for Protein-H of GROup of MAchos and Cynical >> Suckers >> >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> 4 1 1000 1000 1000 >> 7 1 1000 1000 1000 >> 10 1 1000 1000 1000 >> 13 1 1000 1000 1000 >> >> >> and my restraint file for the dummy atoms look like this: >> >> ; position restraints for Protein-H of GROup of MAchos and Cynical >> Suckers >> >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 4942 1 1000 1000 1000 >> 4943 1 1000 1000 1000 >> 4944 1 1000 1000 1000 >> 4945 1 1000 1000 1000 >> >> >> What is wrong? >> > > Atom numbering is done per [moleculetype] and has nothing to do with the > atom > numbers in the coordinate file. If you have a one-atom dummy > [moleculetype], > then the only valid content of posre_memb.itp is: > > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 >
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