[gmx-users] protein complex

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 11/1/15 9:29 PM, Sana Saeed wrote:
> i followed steps of single protein simulation for my protein complex but after
> pdb2gmx when i see the topology file , it only have information of one chain...
> other chains are disapeared. are there any special options for complexes in pdb2gmx?
>

No, but to get any useful advice you'll have to tell us what your exact command 
was, what you think "disappeared" (because that's not possible), etc.

pdb2gmx can handle as many protein/DNA/RNA chains as you can throw at it without 
any special effort.

-Justin

>
>
> On Monday, October 19, 2015 8:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 10/19/15 1:21 AM, Sana Saeed wrote:
>  > i am working on complex of a protein , it has 5 chain and i want to simulate
> the whole complex at the same time. can anyone help me in the procedure please.
>
>  >
>
> It's no different than simulating a single protein.
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

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

==================================================