[gmx-users] question

[Justin Lemkul]

On 9/28/15 10:58 AM, Andrew Bostick wrote:
> I obtained my lig.gro using editconf and lig.itp using antechamber.
>
> I added lig.gro to conf.gro (for RNA).
>
> I included  lig.itp to topolo.top file.
>
> Double sids (704, 705) for atom 2525
> Double sids (704, 705) for atom 2526
> Double sids (704, 705) for atom 2527
> Double sids (704, 705) for atom 2528
> Double sids (704, 705) for atom 2529
> Double sids (704, 705) for atom 2530
> Double sids (704, 705) for atom 2531
> Double sids (704, 705) for atom 2532
> Double sids (704, 705) for atom 2533
> Double sids (704, 705) for atom 2534
> Double sids (704, 705) for atom 2535
> Double sids (704, 705) for atom 2536
> Double sids (704, 705) for atom 2537
> Double sids (704, 705) for atom 2538
> Double sids (704, 705) for atom 2539
> Double sids (704, 705) for atom 2540
> Double sids (704, 705) for atom 2541
> Double sids (704, 705) for atom 2542
> Double sids (704, 705) for atom 2543
> Double sids (704, 705) for atom 2544
> Double sids (704, 705) for atom 2545
> Double sids (704, 705) for atom 2546
> Double sids (704, 705) for atom 2547
> Double sids (704, 705) for atom 2548
> Double sids (704, 705) for atom 2549
> Double sids (704, 705) for atom 2550
>
> The above atom number are related to atoms in ligand.
>

This suggests a topological mismatch with the ligand coordinates.  IIRC, "double 
sids" is related to constraints.

-Justin

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

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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