Re: [AMBER] how to generate the force fied file of AsO3H3?

From: <>
Date: Wed, 29 Nov 2017 22:20:50 +0800

Thanks a lot!
1. 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. 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
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, and searched on "arsenious acid force field". The
following looks like a useful starting point:
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Received on Wed Nov 29 2017 - 06:30:02 PST
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