Re: [AMBER] Arsenic force field parametrization

From: Andrew Schaub <aschaub.uci.edu>
Date: Sat, 16 May 2015 22:55:13 -0700

Another option for forcefield parametrization is the RED Server. I use
http://q4md-forcefieldtools.org/REDServer-Development/ . There is a
tutorial on how to use the server:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
Francois on the RED mailing list just responded to someone also dealing
with arsenic parameter issues a few days ago. He suggested they look at
the following tutorial as a guide to parametrize arsenic using the RED
Server, http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf

On Fri, May 15, 2015 at 12:03 AM, Sushi Shilpa <sushishilpa.gmail.com>
wrote:

> Dear Amber users.
>
> I want to simulate a protein which has Arsenic binding to three cystiens, I
> read the discussions about metalion forcefield parametrization using MCPB
> and MCPB.py. Since metaloid is binding with three cystiens which model I
> should use bonded model or non bonded model. if yes I don't have Gaussian
> program, Is there any other way for geometry optimization.
>
>
> Thanks in advance
>
>
> Regards
>
> Shilpa T
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-- 
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu  <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Sat May 16 2015 - 23:00:02 PDT