Thank you Dr. Martins. Eu aprecio sua ajuda. --Farid
16.09.2014, 16:40, "João Martins" <joaomartins...@gmail.com>: > Unless specified in your mdp that you're using position restraints, by > default it won't use them. > > The command is: > > define = -DPOSRES > > and you should see: > > ; Include Position restraint file >> #ifdef POSRES >> #include "posre_Protein_chain_A.itp" >> #endif > > either after the molecule topology inside the .top file or at the end of a > separate topology file loaded by the top file, depending on which version > you're using. By the way, that's automatic, nothing wrong with the .rtp, > pdb2gmx just creates a position restraint file for heavy atoms > automatically by default. When in doubt, check the manuals. > > *Joao Martins* > > joaomartins...@gmail.com > > On Tue, Sep 16, 2014 at 10:09 AM, Mohd Farid Ismail < > mohd.farid.ism...@yandex.com> wrote: >> Thank you Joao Martins. I figured it out eventually, but it would've been >> easier if the manual is more explicit about this. The oplsaa.ff directory >> for whatever reason doesn't have the residuetypes.dat (Gromacs v. 5.0.1) >> but I got everything to work. >> >> One other question I have, is that pdb2gmx created a .top topology file >> and .itp file that apparently contains the constraints for heavy atoms. I >> don't intend to have these constraints, and I haven't comb the manual or >> search the mailing list yet. Is there anything in the .rtp file that I >> miss? Can I delete these constraints? The system is just a test system of >> 4000 1-propanol, using opls-aa. Any input is appreciated. >> >> Best regards, >> --Farid >> >> 16.09.2014, 14:24, "João Martins" <joaomartins...@gmail.com>: >>> You need to create the R21.rtp and place it in the same folder as your >>> forcefield. You also need to edit your residuetypes.dat inside your >>> forcefield for pdb2gmx to know what to do with that type of molecule. >> Other >>> than that, and if I didn't forget anything, you just need to add any new >>> atomtypes, bond, angles or dihedrals you created for your molecule. >>> >>> *Joao Martins* >>> >>> joaomartins...@gmail.com >>> >>> On Tue, Sep 16, 2014 at 5:45 AM, Mohd Farid Ismail < >>> mohd.farid.ism...@yandex.com> wrote: >>>> Hi, how would one use the .rtp file with pdb2gmx? Is pdb2gmx supposed >> to >>>> just find the .rtp file in the local directory? >>>> >>>> I wanted to create an entry for a new residue using oplsaa. However, >>>> (assuming I build the .rtp file correctly), the pdb2gmx file wouldn't >>>> recognized the residue 'R21' with the error "Residue 'R21' not found in >>>> residue topology file. The file R21.rtp is in the local directory. >>>> >>>> -- >>>> Mohd Farid Ismail >>>> mohd.farid.ism...@yandex.com >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Mohd Farid Ismail >> mohd.farid.ism...@yandex.com >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Mohd Farid Ismail mohd.farid.ism...@yandex.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.