1. could you please tell me what does this mean ? " charge group is inappropriately large" the overall charge is appear to zero in my topology. i am little confused here.
2. if below atoms types in represent C 1&11...so on and those atom types appear in the error.... C opls_240 0 12.011 3 C 0.142 C 0.142 C 0.142 C opls_239 0 12.011 2 C 0.142 C 0.142 and if i cannot see these lines in ffnonbonded.itp do i need to add them in ffnonbonded.itp? On Wed, Jan 22, 2014 at 2:20 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote: > >> Justin, >> >> i was able to generate the .top file for 3 monomers by making the >> corresponding >> .rtp entry. >> >> below is a segment of my .rtp entry and thr .pdb file i used. >> >> .rtp entry for first few atoms out of 208 >> >> [ UNK ] >> [ atoms ] >> >> C1 opls_240 0 1 >> C2 opls_145 -0.12 1 >> C3 opls_240 0 1 >> C4 opls_240 0 1 >> C5 opls_158 -0.12 1 >> C6 opls_158 -0.12 1 >> C7 opls_158 -0.12 1 >> C8 opls_158 -0.12 1 >> C9 opls_158 -0.12 1 >> C10 opls_158 -0.12 1 >> >> > I can almost guarantee that charge group is inappropriately large. Charge > groups generally have no more than 3-4 atoms (see the manual). > > > [ bonds ] >> C1 C2 >> C1 C13 >> C1 C82 >> C2 C3 >> C2 H28 >> C3 C4 >> C3 C5 >> C4 C11 >> C4 C21 >> C5 C6 >> C5 H29 >> >> and so on.... >> >> segment of my .pdb used. >> ATOM 1 C1 UNK 1 -0.3884 0.71623 0.01741 1.00 0.00 >> UNK >> ATOM 2 C2 UNK 1 0.52009 1.96858 0.02142 1.00 0.00 >> UNK >> ATOM 3 C3 UNK 1 2.05261 1.8016 0.02832 1.00 0.00 >> UNK >> ATOM 4 C4 UNK 1 2.67378 0.39693 0.04493 1.00 0.00 >> UNK >> ATOM 5 C5 UNK 1 3.00381 3.01293 0.02021 1.00 0.00 >> UNK >> ATOM 6 C6 UNK 1 2.43967 4.44371 0.06547 1.00 0.00 >> UNK >> ATOM 7 C7 UNK 1 3.74954 5.25409 0.04830 1.00 0.00 >> UNK >> ATOM 8 C8 UNK 1 3.66193 6.78984 0.08175 1.00 0.00 >> UNK >> ATOM 9 C9 UNK 1 5.14612 7.20376 0.05800 1.00 0.00 >> UNK >> ATOM 10 C10 UNK 1 5.41193 8.7194 0.08617 1.00 0.00 >> UNK >> ATOM 11 C11 UNK 1 4.20533 0.24061 0.06162 1.00 0.00 >> UNK >> ATOM 12 C12 UNK 1 5.73704 0.08685 0.07550 1.00 0.00 >> UNK >> ATOM 13 C13 UNK 1 0.24354 -0.6927 0.01957 1.00 0.00 >> UNK >> ATOM 14 C14 UNK 1 -0.6215 -1.9681 0.00425 1.00 0.00 >> UNK >> ATOM 15 C15 UNK 1 -2.1484 -1.7855 0.06322 1.00 0.00 >> UNK >> >> >> i was able to get the .gro and .top file using pdb2gmx >> >> after that i was using grompp but i got an error message as follows. >> >> ERROR 254 [file topol.top, line 1941]: >> No default Ryckaert-Bell. types >> >> >> ERROR 255 [file topol.top, line 1942]: >> No default Ryckaert-Bell. types >> >> >> ERROR 256 [file topol.top, line 1943]: >> No default Ryckaert-Bell. types >> i was reading the gmx_users blogs and it specifies that i need to >> manually enter >> the parameters that have errors. >> >> i am not clear with that. could you please tell me what i need to do >> here. ( >> when i look the lines regarding the errors they >> are pointing out the diheadrals) >> >> > You need to check those lines for what the atom types are for those atoms. > Parameters are not present in ffbonded.itp for that sequence of atoms so > you need to add suitable parameters. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > 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 > > [email protected] | (410) 706-7441 > > ================================================== > -- > 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 [email protected]. > -- Sidath Wijesinghe Graduate Teaching Assistant Dept Of Chemistry Clemson University -- 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 [email protected].
