Dear Shulin Zhuang,
You might be interested in deriving RESP charges using R.E.D.
without/without R.E.D. Server... R.E.D. Server Development
automatically handles iodine (you need to provide the radius for MEP
computation for iodine).
See
http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
regards, Francois
> I performed one MD simulation on triiodothyronine (T3) and its target
> protein. This molecule has three iodine atoms and I use sqm from
> ambertools 1.5 to assign AM1-BCC charge for T3. One reviewer thought that
> AMB-BCC charge is known to be quite inaccurate. This is one of key
> technical questions for the rejection of my publication.
>
>
> After MD simulations, I performed RAMD simulations and RAMD simulations
> revealed some dissociation pathways, some of them were verified by previous
> relevant papers. I think the parameters no problem. The reviewer kindly
> asked me yo provide some quantitative indications that the parameters
> obtained yield reliable or reasonable behavior for the T3 molecule. Could
> anybody tell me how to prove that AM1-BCC charge is reasonable for T3?
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Received on Wed Jan 09 2013 - 01:00:03 PST
