Re: [AMBER] how to change the charge in all_amino94.lib

From: FyD <>
Date: Wed, 03 Nov 2010 21:18:32 +0100

Dear Zhihong,

I think you need to develop a new FF library for molecular fragments
of your new amino-acid (Cys derivative). You can use the R.E.D. Tools
III.4 or R.E.D. Server 2.0 with R.E.D.IV June 2010 & Ante_R.E.D. 2.0.
Tutorials are available as well.


regards, Francois

> In my study, the Cys residue would attack to the ligand and form a
> intermediate.
> Now I would like to run a classical MD simulation for the intermediate.
> Since the resulted intermediate is not a standard residue, I would like to
> treat the intermediate as a CYM residue and a single ligand and then add a
> bond between them.
> However, since the S atom is too negative in CYM, I need to change the
> charge of CYM in all_amino94.lib file.
> I have modified the charge of all the sidechain atoms, and have make the
> sum of the charge equal to 0.
> And I also change the S in all_amino94.prep from "E" to "S", which would
> allow S to form two bonds.
> After that, when I run tleap, it stopped at loading the parameters of CYM.
> Do I miss anything? Or any suggestion to deal with the intermediate?
> Any help would be appreciated!
> Thank you!
> Zhihong

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Received on Wed Nov 03 2010 - 13:30:03 PDT
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