[gmx-users] Assistance required for ligand parameterization

[Justin Lemkul]

On 3/7/14, 4:43 AM, Balasubramani GL wrote:
>
>
> Hi Everyone,
>
>   when i am trying to generate a parameter for ligand using PRODRG. I am
> getting this warning message. is as follows:
>
> PRODRG> WARNING: Multiplicity of generated molecule is not 1.
>
> These are my ligand coordinates:
>
> ATOM 9 NZ LLP X 41 1.600 15.385 12.517 1.00 24.01 N
> ATOM 10 P LLP X 41 4.423 17.845 15.699 1.00 19.86 P
> ATOM 11 O1P LLP X 41 3.370 18.251 14.761 1.00 19.85 O
> ATOM 12 O2P LLP X 41 5.576 18.756 15.639 1.00 19.16 O
> ATOM 13 O3P LLP X 41 3.850 17.679 17.051 1.00 21.16 O
> ATOM 14 O4P LLP X 41 4.941 16.452 15.109 1.00 20.62 O
> ATOM 15 N1 LLP X 41 6.254 13.453 11.662 1.00 23.14 N
> ATOM 16 C2 LLP X 41 4.996 13.033 11.235 1.00 25.17 C
> ATOM 17 C2A LLP X 41 4.873 11.843 10.309 1.00 20.91 C
> ATOM 18 C3 LLP X 41 3.859 13.719 11.685 1.00 24.66 C
> ATOM 19 O3 LLP X 41 2.735 13.314 11.354 1.00 19.33 O
> ATOM 20 C4 LLP X 41 4.005 14.826 12.559 1.00 19.54 C
> ATOM 21 C4A LLP X 41 2.812 15.599 13.054 1.00 21.86 C
> ATOM 22 C5 LLP X 41 5.298 15.201 12.960 1.00 22.65 C
> ATOM 23 C5A LLP X 41 5.578 16.373 13.831 1.00 18.84 C
> ATOM 24 C6 LLP X 41 6.423 14.512 12.530 1.00 23.84 C
> END
>
> can anyone tell me how to fix this problem. Your help is highly
> appreciated.
>

LLP is usually the name of pyridoxal 5'-phosphate in its Schiff base form when 
attached to lysine.  If that is the case here (and judging by the NZ atom name 
and removal of the first 8 atoms, I'm guessing it is), the problem is that 
PRODRG can't decide hybridization states unambiguously because of the the 
truncation of the imino moiety.  You should, at minimum, include the next carbon 
or two in the chain if you want to reasonably parametrize the group.  Of course, 
PRODRG charges need to be re-done anyway, but you'll get a better starting 
point.  Consult the PRODRG FAQ for manually assigning hybridization states; this 
issue is discussed there.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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