AMBER Archive (2008)

Subject: Re: AMBER: about resp charges

From: FyD (
Date: Tue Jun 17 2008 - 07:58:03 CDT

Quoting WanJ Ding <>:

> I am a new user of amber.
> I am trying to get the resp chagres of every atoms in tert-butyloxycarbonyl
> (boc) group. The other paprameters could be found in gaff, but I don't know
> where I could find the corresponding resp charges. Could anyone help me?

I think you need to compute the RESP charge values for the molecule:
and you use an intra-molecular charge constraint (INTRA-MCC) sets to
zero for the NHMe group (NME).

This is straighforward using R.E.D.
See for instance the tutorial
and in particular: Scheme 1

As you can see in Scheme 1 two INTRA-MCC are used to generate RESP
charge values for the central fragment of a new amino-acid. In your
case, you could follow a similar strategy but using a single INTRA-MCC
such as:

   t-Boc-NHMe --R.E.D.-III--> charge values within a force field library
         <--> (Tripos mol2 file format):
     INTRA-MCC = 0 - whole molecule: tBoc-NHMe
                                 - molecule fragment: tBoc
                                   (what you really need)

If you are interested I can run your charge value derivation and force
field library generation using the beta version of the R.E.D.Server
(interface of R.E.D.-IV) we are going to release. It should take 2
minutes ;-)

regards, Francois

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