Thanks Justin. How shall I tackle this problem? Can I use any other AA force field, say CHARMM27? The Aib parameters are available in an old gromacs forcefield (mentioned as "DEPRECATED" in gromacs-4.5.7), which hasn't showed any error while simulating the same system.
On Tue, Jul 28, 2015 at 6:07 PM, Justin Lemkul <[email protected]> wrote: > > > On 7/28/15 3:30 AM, Venkat Reddy wrote: > >> 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? >> >> > No idea. Generally dihedrals are the least transferable of any bonded > parameter, so there's no reason to assume that you can apply the parameters > from other interactions to any other given interaction. > > -Justin > > > 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]. >>> >>> >> >> >> > -- > ================================================== > > 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].
