Very well. Thank you for your assistance :).
2014-08-08 21:00 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 8/8/14, 1:58 PM, Dawid das wrote: > >> Thank you but now I have different type of question. >> If I use -nocmap option for pdb2gmx what impact on the result of my >> simulation? >> >> > Then you won't have CMAP terms, i.e. you'll basically be reverting back to > the old CHARMM22 force field. > > -Justin > > > >> 2014-08-08 19:42 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 8/8/14, 12:39 PM, Dawid das wrote: >>> >>> 2014-08-08 15:48 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >>>> >>>> The problem is in atom naming. You have used MN1 and MC3 for the >>>> >>>>> equivalent of amino acid N and C atoms, respectively. pdb2gmx chokes >>>>> here, >>>>> because Phe-65 tries to make a bond to the +N atom, which it does not >>>>> find >>>>> until it runs into Ser-69. Likewise with the C atom in CH6. If you >>>>> rename >>>>> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works >>>>> fine. >>>>> >>>>> >>>>> OK, I see your point but if I do as you suggest how will I specify >>>> nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and >>>> MC3 >>>> atoms have different vdW and electrostatic parameters than N and C >>>> atoms, >>>> respectively. >>>> >>>> >>>> Realize that atom *names* and atom *types* are separate entities. You >>> have all your names and types the same, which can be confusing. All you >>> need to do is *name* the atom N and assign it a *type* of MNH1 or >>> whatever >>> it was. Parameters are always assigned by type, not name. >>> >>> >>> >>> >>>> If there are still missing parameters for interactions, you'll have to >>>> >>>>> figure that out. There are several missing inter-residue angles and >>>>> dihedrals in your .rtp entry for CH6. >>>>> >>>>> >>>>> Do you mean those which I stated above? >>>> >>>> >>>> Above? You mean in a previous message? Most of those errors were >>> derived >>> from incorrect, nonsensical bonding. >>> >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.