AMBER Archive (2003)

Subject: Re: AMBER: MSE

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 24 2003 - 12:08:59 CST

On Wed, Dec 24, 2003, Wen Li wrote:
>
> In the crystal structure that I am working on, there is modified residue
> MSE which is related to MET (selenomethionine), but labeled as HETATM.
> What is the supposed way to deal with this residue in order to run sander?
>

You need to use LEaP to define a modified residue, MSE, that has the selenium
there in place of sulfur. This will require developing or finding the
appropriate parameters. Once LEaP "knows" about your residue, you can use
loadPdb in the regular way.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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