Hi, Thanks Justin. If you think it useful, then in the CHARMM36 forcefield.itp you could do stuff like
#if (defined _FF_GROMOS96) || ... #error Do not attempt to mix another force field with CHARMM36, it is self-contained #endif getting the magic strings from the other share/top/*/forcefield.itp files. Or does this make sense to do generally, e.g. by giving grompp the smarts to refuse to #include another forcefield.itp file (or maybe refuse to let another distinct _FF_* to be #defined)? That doesn't stop people going directly to "#include ffbonded.itp," but you can't save every lemming... :-) Mark On Tue, May 5, 2015 at 3:16 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/5/15 8:09 AM, A. mohammadzadeh wrote: > > i used output file that made by charmm-gui for gromacs but gave me the > > same error. > > > > For the purpose of completing the thread: Do not modify any topology file > provided by CHARMM-GUI. In this case, the OP #included another force > field and > broke the format. CHARMM-GUI provides self-consistent force field files > that > rely on nothing else. > > -Justin > > > On Tue, May 5, 2015 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> On 5/5/15 7:35 AM, A. mohammadzadeh wrote: > >> > >>> Hello. i have a problem could you help me to > >>> solve it pleas? > >>> > >>> > >>> i used charmm server to get the parameters for my new membrane with > dppc > >>> and cholestrol - > >>> > >>> i converted it into the gromacs topology. > >>> > >>> > >> What does "converted" mean? I'm assuming you're using CHARMM-GUI, but > >> that means you don't need any conversion. We provide all of the inputs > >> (.mdp, coordinates, topology) that should be used directly. > >> > >> When I try grompp: > >>> > >>> > >>> WARNING 23 [file charmm36.itp, line 41]: > >>> Overriding atomtype SOD > >>> > >>> > >>> WARNING 24 [file charmm36.itp, line 201]: > >>> Overriding non-bonded parameters, > >>> > >>> old: 0.290767 0.0906104 0.290767 0.0906104 new > >>> CTL1 SOD 1 2.94954293108e-01 9.06104103511e-02 > >>> > >>> WARNING 25 [file charmm36.itp, line 222]: > >>> Overriding non-bonded parameters, > >>> > >>> old: 0.290767 0.0906104 0.290767 0.0906104 new > >>> CTL2 SOD 1 2.94954293108e-01 9.06104103511e-02 > >>> > >>> WARNING 26 [file charmm36.itp, line 242]: > >>> Overriding non-bonded parameters, > >>> > >>> old: 0.290767 0.0906104 0.290767 0.0906104 new > >>> CTL3 SOD 1 2.94954293108e-01 9.06104103511e-02 > >>> > >>> WARNING 27 [file charmm36.itp, line 261]: > >>> Overriding non-bonded parameters, > >>> > >>> old: 0.290767 0.0906104 0.290767 0.0906104 new > >>> CTL5 SOD 1 2.94954293108e-01 9.06104103511e-02 > >>> > >>> WARNING 28 [file charmm36.itp, line 498]: > >>> Overriding Proper Dih. parameters. > >>> Use dihedraltype 4 to allow several multiplicity terms. > >>> > >>> old: 180 4.184 1 180 4.184 1 > >>> new: CEL1 CEL1 CTL2 CEL1 9 0.000000e+00 4.016640e-01 4 > >>> > >>> > >> The solution to the problem depends on what you mean by "converted" > above. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 629 > >> 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 629 > 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? 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