Thank you Justin for clear explanation. However, the parameters are available for CX CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.000 0.000; C* CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.000 0.000 ; So, can I apply the same for CT-CT_2-CT-HC dihedral?
Thank you for your valuable time and concern. On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul <[email protected]> wrote: > > > On 7/27/15 1:21 AM, Venkat Reddy wrote: > >> 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? >> >> > You're confusing atom names and atom types. The names are totally > irrelevant for parameter assignment. The CB2-C1-CB1-HB11 dihedral has a > sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140, which > have bonded types (see second column of ffnonbonded.itp) of CT-CT_2-CT-HC. > So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in > ffbonded.itp. > > -Justin > > > 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]. >>> >>> >> >> >> > -- > ================================================== > > 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].
