[gmx-users] Setting custom atoms in FF

[Justin Lemkul]

On 3/29/15 7:53 PM, Alex wrote:
> Another question about x2top: in the previous discussion, the atom
> type was determined from its environment and the element type. What if
> I set up my PDB with atom labels (i think that's the third field from
> the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the
> force field contains
>
> CJ1   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> CJ2   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149
>
> Will then the right distinction be made? I'm asking before trying
> it, because it is quite tedious for me to do the labeling. The
> issue is way beyond carbons, I just discovered that a bunch of
> different atoms isn't set up correctly.
>

The element field can be up to 16 characters long, per the code (overkill, but 
it indicates that there should be some flexibility).

-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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