[gmx-users] simulating only few residues from whole protein]

[Justin Lemkul]

On 3/19/13 4:13 AM, preetichoudhary at iisermohali.ac.in wrote:
>
>
>
> ---------------------------- Original Message ----------------------------
> Subject: simulating only  few  residues from whole protein
> From:    preetichoudhary at iisermohali.ac.in
> Date:    Tue, March 19, 2013 10:45 am
> To:      gmx-users at gromacs.org
> --------------------------------------------------------------------------
>
>
>
>
> ---------------------------- Original Message ----------------------------
> Subject:
> From:    preetichoudhary at iisermohali.ac.in
> Date:    Tue, March 19, 2013 10:44 am
> To:      gmx-users at gromacs.org
> --------------------------------------------------------------------------
>
> Hi,
> can anyone tell me how to carry out simulations in which we take the whole
> protein pdb structure but simulate only a certain part of it(only some
> residues).???? what will be the mdp files for such simulations ???
> please help me if you know how to do it.
>

Do you want to extract certain residues from the structure and simulate those, 
or just try to fix the positions of some residues while allowing others to move? 
  In the latter case, use freezegrps or position restraints.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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