Dear Rinsha Chk,
> I’m performing a QM/MM calculation on a protein model, in which
> some of the amino acids are neutralised for my purpose. The problem is that
> I’m unable to assign the Amber94 charges for the additionally added atoms,
> (oxygen and hydrogen of OH of acidic end). How can I get those charges? I
> searched literature but end up with unfruitful result....
W.D. Cornell, P. Cieplak, C.I. Bayly & P.A. Kollman J. Am. Chem. Soc.
1993, 115, 9620-9631.
C.I. Bayly, P. Cieplak, W.D. Cornell & P.A. Kollman J. Phys. Chem.
1993, 97, 10269-10280.
P. Cieplak, W.D. Cornell, C.I. Bayly & P.A. Kollman J. Comput. Chem.
1995, 16, 1357-1377.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
You could use PyRED at RED Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#2
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25
regards, Francois
F.-Y. Dupradeau
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http://q4md-forcefieldtools.org/FyD/
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Received on Fri Apr 13 2018 - 22:00:02 PDT
