Dear Justin, Thank you for the prompt reply. I have checked the topology file once again and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate the dihedral parameters for the above mentioned dihedral angle in ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So, can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?
On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul <[email protected]> wrote: > > > On 7/24/15 9:20 AM, Venkat Reddy wrote: > >> Dear all, >> I am trying to simulate a peptide with engineered residues like Aib (alpha >> amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though >> everything went well initially during topology generation, grompp showed >> the following error. >> >> ERROR 1 [file topol.top, line 2316]: >> No default Ryckaert-Bell. types >> ERROR 2 [file topol.top, line 2317]: >> No default Ryckaert-Bell. types >> ERROR 3 [file topol.top, line 2318]: >> No default Ryckaert-Bell. types >> ERROR 4 [file topol.top, line 2325]: >> No default Ryckaert-Bell. types >> ERROR 5 [file topol.top, line 2326]: >> No default Ryckaert-Bell. types >> ERROR 6 [file topol.top, line 2327]: >> No default Ryckaert-Bell. types >> >> The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11 is >> throwing the error. My question is, even though the parameters for Aib are >> available in OPLS ff, why I am getting this error? >> >> > grompp doesn't lie. Either you're looking at the wrong lines or you're > looking at the wrong parameters. Some residues are constructed for > convenience but if they're not "official" then there may be problems. > > -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 > > [email protected] | (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 [email protected]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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].
