[gmx-users] How to have two proteins randomly positioned and oriented in the box
caizkun at gmail.com
Mon Apr 1 13:35:10 CEST 2013
Thank you, Justin. Your online tutorial helped me a newbie a lot.
I ever tried using genbox -ci -nmol to insert two proteins in a specific
box. But it didn't work. Nothing was inserted into the box. Maybe enlarging
the box would work. I would try.
On Mon, Apr 1, 2013 at 10:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/31/13 9:51 PM, Zhikun Cai wrote:
>> Hi everyone,
>> I am trying to insert two same proteins in a simulation box. Now I have
>> used pdb2gmx to convert one protein's pdb file to gro file. Then how
>> I do? How could they be randomly positioned and oriented in the box?
> Place them however you like within the box using editconf -center,
> -translate, -rotate, etc as necessary. You may be able to get completely
> random insertion with genbox -ci -nmol, but I've never tried it with a
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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