[gmx-users] OPLS forcefield amide charge

[Justin Lemkul]

On 8/27/15 7:13 PM, Stella Nickerson wrote:
> I am simulating a polymer using the OPLS forcefield. The polymer has a
> sidechain with a secondary amide. Using the atom charges given in the
> forcefield, the amide group (N, O, 2Cs, 2 Hs) has a net negative charge. I
> don't understand why this is so, since to my knowledge amides are not
> generally negatively charged. When repeated several times, the sidechain
> gives my polymer a net negative charge, when in real life the polymer is
> neutral.
>

An amide is neutral.  Your above atom list is missing H atoms, though:

CHn-C(=O)-NH2

For instance, Gln:

     CG    opls_136   -0.120     3
    HG1    opls_140    0.060     3
    HG2    opls_140    0.060     3
     CD    opls_235    0.500     4
    OE1    opls_236   -0.500     4
    NE2    opls_237   -0.760     5
   HE21    opls_240    0.380     5
   HE22    opls_240    0.380     5

Net neutral.

-Justin

> I'm not sure what to do. I don't want to just arbitrarily adjust the
> charges in the forcefield, but I don't understand why the forcefield
> charges work out this way unless the forcefield is flawed.
>
> Can I just slightly adjust the charges in the amide group to come out
> neutral. That seems... wrong.
>

-- 
==================================================

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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