[gmx-users] parameter for repeating units with cgenff
jalemkul at vt.edu
Sat Dec 12 19:35:26 CET 2015
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 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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