CCL: Heating Locally in MD
- From: "Ross Walker" <ross],[rosswalker.co.uk>
- Subject: CCL: Heating Locally in MD
- Date: Mon, 16 Jan 2006 17:01:55 -0800
Sent to CCL by: "Ross Walker" [ross]=[rosswalker.co.uk]
Dear Charles,
If you have a copy of AMBER then you can do this using a number of methods,
probably the most reliable being restraints. You could first of all minimise
the entire protein, then heat it to 10K with no restraints. Then you could
add weak harmonic restraints say 5 KCal/mol/A to everything you want to fix
and then heat the system to 300K. By doing things this way you should attain
the correct kinetic energy ensemble for the enzyme since.
A tutorial on how to do this sort of thing in AMBER is available here:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/index.htm
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-chemistry#,#ccl.net [mailto:owner-chemistry#,#ccl.net]
> Sent: Monday, January 16, 2006 16:32
> To: Walker, Ross
> Subject: CCL: Heating Locally in MD
>
> Sent to CCL by: Charles Hu [umchhu]=[yahoo.com]
> --0-1539825457-1137445232=:78507
> Content-Type: text/plain; charset=iso-8859-1
> Content-Transfer-Encoding: 8bit
>
> Dear CCLers,
>
> I am novice user here and would like to do some molecular
> dynamics calculation of an enzyme, with special requirement
> that only heating a part of the protein and freeze the rest.
> i.e., after minimizing and equilibrating the whole protein at
> 10K, only thermalize the active site of the enzyme to 300K.
>
> I am wondering which MD package could that. If possible, I
> prefer to free software such as TINKER.
>
> Thank you very much!
>
>
>
>
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> --0-1539825457-1137445232=:78507
> Content-Type: text/html; charset=iso-8859-1
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>
> <div id="RTEContent">Dear CCLers,<br><br>I am
novice user
> here and would like to do some molecular dynamics calculation
> of an enzyme, with special requirement that only heating a
> part of the protein and freeze the rest. i.e., after
> minimizing and equilibrating the whole protein at 10K, only
> thermalize the active site of the enzyme to 300K.
> <br><br>I am wondering which MD package could that. If
> possible, I prefer to free software such as TINKER.
> <br><br>Thank you very
much!<br><br></div><p>
> <hr size=1>Yahoo! Photos - Showcase holiday
> pictures in hardcover<br>
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://pa.yahoo.com/>
*http://us.rd.yahoo.com/mail_us/taglines/photos/evt=38088/*htt
p://pg.photos.yahoo.com/ph//page?.file=photobook_splash.html">> Photo
Books</a>. You design it and we'll bind it!
> --0-1539825457-1137445232=:78507--
>
>
>
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