Re: about the MSE residue

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 27 2006 - 08:42:39 CST

Dear Shulin,
the parameters you've linked to are xplor parameters, not charmm
parameters, so they're not really compatible. You'll have to find (or
make) charmm parameters to get it to work.

However... are you sure that you actually want to do your simulations
with MSE in there? Usually selenomethionine is only present in a protein
to aid the crystallographers in obtaining phase information, and should
actually be methionine in the native structure.

Peter

Shulin Zhuang wrote:

> Dear All,
>
> My pdb file contains a MSE residue. When I use the top_all22_prot.inp
> in psfgen program to generate the psf file of this protein,
> psfgen complain that " unknown residue type MSE".
>
> I check the top_all22_prot.inp and par_all22_prot.inp, there is no
> parameter for MSE. Fortunately, I find its parameters in the following
> links:http://xplor.csb.yale.edu/xplor/hetero/MSE.html
> <http://xplor.csb.yale.edu/xplor/hetero/MSE.html>
> I want to know whether these parameters are appropriate and how to add
> them to top_all22_prot.inp and par_all22_prot.inp. Should I just copy
> them and paste them to top_all22_prot.inp and par_all22_prot.inp? Is
> there any other thing need to be done?
>
> Looking forward to the suggestions.
>
> Thanks
>
> --
> Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> shulin.zhuang_at_gmail.com <mailto:shulin.zhuang_at_gmail.com>

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