[gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 10:17 AM, gromacs query wrote:
> Hi All,
>
> I am using cgenff to derive parameters for some polymer (A-BBBB...-C). The
> repeating block B has some Oxygen O atom which joins the next residue
> (-BO-). When I derive charges for B residue with cgenff then I get net -1
> charge on B residue because of this unsatsified O atom. I want to keep B
> residue formal charge zero. I get formal charge zero if I derive charges on
> B-OH residue but removing H will again will give some non-intergral formal
> charge. I am not sure what should done in this regard.
>
> If someone has some experience with this or suggestion I will highly
> appreciate it.
>

To derive suitable monomer units, you have to include all the linking atoms; if 
it's an ether of some sort, you need B-O-CH3 or whatever is similar to then 
apply to the actual polymer itself.  Just parametrizing B in the absence of 
flanking atoms is inappropriate.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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