[gmx-users] questions on ligand.gro and ligand.itp preparation

[Justin Lemkul]

On 4/29/16 2:50 AM, Brett wrote:
> Dear All,
>
>
> Here I have 2 questions related to the ligand.gro and ligand.itp preparation for the md of protein-ligand complex.
>
>
> First, we have different ways to get the ligand.itp by different serves which use different electronic charge assignment methods. Is any difference for the md result for the whole protein-ligand complex if we use ligand.itp got by different charge assignment methods?
>

Yes, in some cases it is dramatic.

>
> Second, in the Justin on-line tutorial for the md of protein-ligand, it has the method to edit the complex.gro, for example the Justin tutorial final format was:
> 163ASN      C 1691   0.621  -0.740  -0.126
> 163ASN     O1 1692   0.624  -0.616  -0.140
> 163ASN     O2 1693   0.683  -0.703  -0.011
> 1JZ4 C4 1 2.429 -2.412 -0.007
> 1JZ4 C14 2 2.392 -2.470 -0.139
> 1JZ4 C13 3 2.246 -2.441 -0.181
> ......
> 5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000   0.00000
>
>
> My question is, suppose we have an artificial lysozyme which contains 2 lysozyme subunit, each subunit binding one JZ4, then how do we edit the complex.gro? Does the final complex.gro change into something like?
>
>
> 163ASN      C 1691   0.621  -0.740  -0.126
> 163ASN     O1 1692   0.624  -0.616  -0.140
> 163ASN     O2 1693   0.683  -0.703  -0.011
> 1JZ4 C4 1 2.429 -2.412 -0.007
> 1JZ4 C14 2 2.392 -2.470 -0.139
> 1JZ4 C13 3 2.246 -2.441 -0.181
> ....
> 2JZ4 C4 (followed by coordinates)
> 2JZ4 C14 (followed by coordinates)
> 2JZ4 C13 (followed by coordinates)
> 5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000   0.00000
>

The order is irrelevant, as long as the coordinate file matches the topology.

-Justin

>
> I am looking forward to getting your reply.
>
>
> Brett
>
>

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

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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