[gmx-users] How to have two proteins randomly positioned and oriented in the box

[Zhikun Cai]

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
>> should
>> 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
> protein.
>
> -Justin
>
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> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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