Thank you for your kind help!
Another question is,
how about using QM/MM to study peptide and AsO3H3 interaction?
I searched online and found others used ONIOM method to perform QM/MM calculations for AsO3H3 containing system.
But the amber tutorials tell me, before QM/MM calculations, typing system force field is asked.
I cannot understand,
why still need to generate force field parameters for QM part, which mainly depends on QM software?
Or did I miss anything important about qm/mm in amber?
Looking forward to hear your reply.
Best wishes
Yuan Min
> -----原始邮件-----
> 发件人: "Andrew Schaub" <aschaub.uci.edu>
> 发送时间: 2017-11-30 00:57:55 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] how to generate the force fied file of AsO3H3?
>
> 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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> >
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Received on Wed Nov 29 2017 - 20:00:04 PST
