Re: Re: phosphotyrosine

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Mon Jun 20 2011 - 06:30:03 CDT

Hi Bharat,

You can apply patches in generating input files using psfgen. See
www.ks.uiuc.edu/Research/vmd/plugins/psfgen and the namd tutorial
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html
for info.

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Sun, Jun 19, 2011 at 8:26 PM, bharat gupta <bharat.85.monu_at_gmail.com> wrote:
>
> Hi,
> I have  a docked complex of my protein with phosphotyrosine, Now I want to carry out simulation with that in order to predict the binding affinity. I have found out that CHARMM FF has some patch for PTYR, but I don't know how to use it ??... can anybody help me
>
> --
> Bharat

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