Re: [AMBER] Deprotonated serine residue.

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 26 Oct 2016 10:27:42 +0200

Dear Dading Huang,

> I want to simulate a protein that contains a deprotonated serine residue.

you could create your own force field - residue...

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26

and use http://q4md-forcefieldtools.org/REDServer-Development/

You will likely have to create a new atom type for that O(-) oxygen.

See http://q4md-forcefieldtools.org/Tutorial/Mini-HowTo-InputFiles.pdf
then once you got the QM data re-run PyRED using the Re_Fit job to
generate/update the FF.
see http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf

regards, Francois


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


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Received on Wed Oct 26 2016 - 01:30:02 PDT