Re: [AMBER] Issue with running sander with SHAKE

From: David A Case <case.biomaps.rutgers.edu>
Date: Tue, 29 Nov 2011 15:15:32 -0500

On Tue, Nov 29, 2011, Andrew Voronkov wrote:

> I've got a simple solution from Yue Yang from MCBP team.
> When I place zinc atom right after the protein, not after the ligand
> there is no such issue. In general I didn't thought it may make a
> difference as far as TER records are ok, but it looks like the order in
> which zinc and ligand records are mutually placed makes difference.

I'm glad it works. If you have a chance, please post an example if you can,
since we should try to fix the problem. LEaP should not be requiring any
"magic" order for the various parts of the pdb file.

...thanks...dadc


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Received on Tue Nov 29 2011 - 12:30:03 PST
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