Re: [AMBER] Metal geometry

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 09 Apr 2016 10:19:01 +0200

Dear Vince,

You could use PyRED at R.E.D. Server Dev. to generate the required
force field:
http://upjv.q4md-forcefieldtools.org/REDServer-Development/

See Tutorials:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf

regards, Francois


> Is it possible to obtain proper tetrahedral metal geometry for a modified
> peptide, whose structure was calculated using nmr restraints and using
> AMBER in restrained MD method.
> I am currently using non-boded ZAFF model to handle zinc. In my calculation
> of 200ps rMD in GB model metal geometry is deviated from ideal geometry
> (tetrahedral to trigonal bipyramidal). For the moment I have removed the
> nmr restraints in the coordination, because on the ligand peaks was not
> identified due to sever overlap and since bond between ligands were
> defined. Could any one suggest me in solution NMR structure is it possible
> to maintain geometry in rMD protocol.




           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


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Received on Sat Apr 09 2016 - 01:30:05 PDT
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