Dear Shilpa,
Sorry for the late reply due to I am a little bit busy these days.
Do you expect the coordinate number to change or not for the metal site? If
no change, I recommended you to use the bonded model.
I am trying to add support for ORCA, a charge-free QM program from MCPB.py.
The related change will be added into AmberTools15 in future bugfix.
Best,
Pengfei
2015-05-17 1:55 GMT-04:00 Andrew Schaub <aschaub.uci.edu>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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/>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 18 2015 - 14:30:02 PDT
