pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter > 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) > 1: TIP4P TIP 4-point, recommended > 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) > 1: PRO-ZWITTERION_COO- (only use with zwitterions containing exactly one residue)
(I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) but the result was the same) Screen-out: http://pastebin.com/CuMa7aZ7# topology: http://pastebin.com/FSbcFGYR Thanks in advance, Kevin On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/1/15 12:09 PM, Kevin C Chan wrote: > >> Thanks Justin, >> >> I did not but I tried just now. The aforementioned dihedral terms remain >> along with the errors. >> >> > Please provide your full pdb2gmx command, all screen output, and full > topology. Use file sharing services, pastebin, etc. as needed. > > -Justin > > > Thanks in advance, >> Kevin >> >> On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 6/1/15 10:57 AM, Kevin C Chan wrote: >>> >>> Dear Users, >>>> >>>> I am testing with OPLSSaa force-field of proline. First I arbitrarily >>>> extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro >>>> and >>>> top are however not suitable for further grompp (even minimization). The >>>> error messages are as follows: >>>> >>>> ERROR 1 [file topol.top, line 161]: >>>> No default Ryckaert-Bell. types >>>> >>>> When I look into the line 161, it refers to a dihedral term concerning >>>> (CD >>>> N CA C) which is not able to be found in ffbonded.itp. However, other >>>> dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not >>>> found in itp do not report such error and I was successful to grompp >>>> after >>>> commenting out the line 161. >>>> >>>> Why would this happen? >>>> >>>> >>>> Did you choose the proper "PRO-ZWITTERION-*" termini when running >>> pdb2gmx? >>> >>> -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? 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.