I posted on arsenic a couple of years ago:
rom: Andrew Schaub
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 Wed, Nov 29, 2017 at 6:28 minyuan.mail.ustc.edu.cn <
minyuan.mail.ustc.edu.cn> wrote:
> Thanks a lot！
> 1. http://pubs.acs.org/doi/pdf/10.1021/jp2051245 says that there is
> difference between As and P.
> It compares the two systems at QM level.
> Calculated interaction energies between As (P) and a water, As (P) and an
> alkali/ alkaline-earth metal cation.
>
> 2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337691/#notes-1 does
> force field modification via replacing As with P.
>
> However, it still remains unclear how to merge AsO3H3 parameters into
> force field file of peptide.
>
>
> Best wishes
> Yuan Min
>
>
> minyuan.mail.ustc.edu.cn
>
> From: David A Case
> Date: 2017-11-29 20:38
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to generate the force fied file of AsO3H3?
> On Wed, Nov 29, 2017, Bill Ross wrote:
>
> > > I want to put a small molecule (AsO3H3) into a peptide PDB file.
> > Maybe you can adapt GAFF params.
>
> GAFF only goes up to phosphorus.
>
> Don't forget that several companies offer free services that will search
> the internet to see what others have done in similar circumstances. I
> used google.com, and searched on "arsenious acid force field". The
> following looks like a useful starting point:
>
> www.ncbi.nlm.nih.gov/m/pubmed/21923105/
>
> ....dac
>
>
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Received on Wed Nov 29 2017 - 09:00:02 PST
