Due to reasons, would it be possible for you to suggest off-list? I will really appreciate.
Thanks. On Sat, Dec 12, 2015 at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/12/15 1:25 PM, gromacs query wrote: > >> Hi Justin >> >> Somehow I can not use available units in CHARMM library. The best thing I >> could achieve as of now is using CGenFF. I created a side chain terminated >> with some atoms (cap) which are same as in the next attaching unit >> (directly available in CHARMM). After removing caps from the side chain >> and >> some atoms from second attaching unit I can generate a full combined unit >> but with formal net charge being 0.002. This seems to be very less but can >> I spread this charge (manually) on other atoms to get a nice 0.000 formal >> charge as this residual charge will add up as I have many such units. I >> have tried different combinations but this is the minimal formal charge I >> was able to achieve. >> >> > There should be a way to assign the charges intuitively if you have capped > the units appropriately. Without knowing the chemical structure you're > working with, I can't (and won't) blindly suggest anything. > > > -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. > -- 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.