Hi Shilpa,
I checked the ORCA program and found that it could generate Hessian matrix
very easily, which can be used for the force constant calculation. But it
could not perform Merz-Kollman charge calculation. There is a replacement
for that which is called CHELPG charge calculation, but it is not easy to
generate the charge points on the surface of molecule for the procedures
are complicated, while these points are needed for the RESP charge fitting.
So up to now ORCA can not be a totally replacement for Gaussian. I will
still try to find free-charge replacement in the future.
Best,
Pengfei
2015-05-18 17:18 GMT-04:00 Pengfei Li <ambermailpengfei.gmail.com>:
> 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
>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Wed May 27 2015 - 08:30:02 PDT
