AMBER Archive (2008)

Subject: Re: AMBER: chromophore parameters for Molecular Dynamics

From: FyD (
Date: Wed Jan 16 2008 - 08:59:31 CST

Quoting Anthony Cruz <>:

> Thank you for you rapidly responce. If you have time I want to ask you a
> question about the charge derivation. The chromophore was made from the
> cyclization of THR-TYR-GLY
> ( It have the
> side chains of the THR and GLY.

In your chromophore, you have a Thr instead of a Ser, if I understand you.

> During the charge derivation procedure could
> be good idea to do intra-molecular charge constraint in this sidechains or
> only on the N-H and C-O terminal atoms?

Sorry, I am not sure to understand you...

A good way to see if an intra-molecular charge constraint (INTRA-MCC)
can be applied in a RESP fit for a chemical group "X" is to do the fit
without this INTRA-MCC in a 1st step.
=> Then, compare the total charge value you get in the fit without the
INTRA-MCC for this chemical group "X" (i.e. manually calculate it) to
the value of the INTRA-MCC you wish to apply in a 2nd step/fit (for
this chemical group "X"). More the two values will be similar, better
will be your 2nd fit (i.e. the fit with the INTRA-MCC) & consequently
better will be your RRMS value.

Applying this, in two R.E.D. runs is straighforward:
Just add the INTRA-MCC keyword at the beginning of the line to run the
job with this INTRA-MCC, & add just a space character in front of the
INTRA-MCC keyword to run the job without this INTRA-MCC; i.e. in the
.p2n file, you do:

   INTRA-MCC 0.0 | 1 2 etc... | K to run the fit without this INTRA-MCC
INTRA-MCC 0.0 | 1 2 etc... | K to run the fit with this INTRA-MCC

regards, Francois

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