True, true. :) On Wed, Apr 1, 2015 at 2:29 PM, Justin Lemkul <[email protected]> wrote:
> > > On 4/1/15 4:27 PM, Alex wrote: > >> I think I solved it already, thanks. Entirely due to horrible mess created >> by the necessity to create custom atom types. I wish you guys could make >> the bond length tolerance an input to x2top, I really do. :) >> >> > Well, I already showed you the function to modify to change it to your > heart's desire ;) > > -Justin > > > On Wed, Apr 1, 2015 at 2:18 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 4/1/15 2:03 PM, Alex wrote: >>> >>> I am working with a local copy of oplsaa.ff where I have defined a set >>>> of >>>> custom atom types in atomname2type.n2t and added the bond and angle >>>> parameters into ffbonded. x2top creates the topology without issues, but >>>> grompp reports a fatal error (see subject). >>>> The particular type it complains about is actually opls_335. Gromacs v. >>>> 4.6-beta3. Any ideas? >>>> >>>> >>>> Don't use beta versions, especially ancient ones. >>> >>> The problem is related to a translated type; note that in ffnonbonded.itp >>> the second column is an atom type that is used in ffbonded.itp. These >>> are >>> different from the nonbonded types, but since there are fewer bonded >>> types >>> to cover the parameters, these are used to remove redundancy. >>> >>> -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]. > -- 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].
