[gmx-users] on atom types related to ligand

[Justin Lemkul]

On 5/6/16 5:39 AM, Brett wrote:
> Dear All,
>
>
> By ACPYPE (antechamber), I got the following gro files for ADP with AMBER (GAFF) force fields:
>
> 1 ADP O2A 1 11.124 10.200 13.406
> 1 ADP PA 2 11.135 10.260 13.268
> 1 ADP O1A 3 11.011 10.309 13.198
> 1 ADP O3A 4 11.237 10.383 13.274
> 1 ADP PB 5 11.182 10.530 13.312
> 1 ADP O1B 6 11.142 10.599 13.184
> 1 ADP O2B 7 11.081 10.516 13.422
> 1 ADP O3B 8 11.312 10.600 13.375
> 1 ADP O5' 9 11.205 10.152 13.171
> 1 ADP C5' 10 11.133 10.037 13.127
> 1 ADP C4' 11 11.124 9.933 13.239
> 1 ADP C3' 12 11.144 9.790 13.192
> 1 ADP O3' 13 11.273 9.740 13.231
> 1 ADP C2' 14 11.030 9.711 13.255
> 1 ADP O2' 15 11.073 9.590 13.318
> 1 ADP C1' 16 10.970 9.807 13.358
> 1 ADP O4' 17 10.996 9.937 13.304
> 1 ADP N9 18 10.825 9.785 13.390
> 1 ADP C4 19 10.757 9.854 13.482
> 1 ADP C5 20 10.620 9.800 13.485
> 1 ADP N7 21 10.618 9.701 13.394
> 1 ADP C8 22 10.741 9.692 13.338
> 1 ADP N3 23 10.786 9.958 13.566
> 1 ADP C2 24 10.694 10.008 13.651
> 1 ADP N1 25 10.567 9.963 13.657
> 1 ADP C6 26 10.524 9.861 13.579
> 1 ADP N6 27 10.397 9.817 13.588
> 1 ADP HO3' 28 11.283 9.662 13.202
> 1 ADP HO2' 29 11.152 9.599 13.345
> 1 ADP HN62 30 10.342 9.854 13.643
> 1 ADP HN61 31 10.370 9.752 13.538
> 1 ADP H5'2 32 11.044 10.062 13.098
> 1 ADP H5'1 33 11.178 9.998 13.050
> 1 ADP H8 34 10.766 9.628 13.270
> 1 ADP H4' 35 11.196 9.958 13.300
> 1 ADP H3' 36 11.142 9.781 13.095
> 1 ADP H2' 37 10.966 9.683 13.188
> 1 ADP H2 38 10.720 10.081 13.709
> 1 ADP H1' 39 11.011 9.794 13.445
> 0.97060 1.01010 0.65970
>
>

> Then I check the atopetypes.atp, including the atp file for amber force
> fields. By my lacking knowledge, in the atp files, I cannot find atom types as
> O2A, O3A, PA. Will you please tell me the meaning of "A" in O2A, O3A and PA? How

Coordinate files contain atom names, not atom types, so naturally you will not 
find these in the .atp file.  Moreover, GAFF assigns atom types (when you find 
them in the actual topology) that are distinct from the parent AMBER force 
field; this is done by design to avoid clashes.

> about O5'? what is the meaning of the Apostrophe in O5'? And why there is no N9

Standard nucleic acid nomenclature.  Primes are added to sugars, and nucleoside 
di/triphosphates have their phosphates labeled as alpha (A), beta (B), and gamma 
(G).

-Justin

> in the atp files?
>
>
> I am looking forward to getting a reply from you.
>
>
> Brett
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-- 
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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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