AMBER Archive (2004)

Subject: Re: AMBER: Use of RED

From: FyD (fyd_at_u-picardie.fr)
Date: Fri May 28 2004 - 15:20:42 CDT

> I write because I am trying to reproduce the charges of the
> aminoacids
> that were calculated with RESP using ACE and NMA as blokcing groups.
> When using the RED program I need the following constraints:
>
> -ACE, NMA and the aminoacid must be neutral
> -The C=O of the aminoacid should have the same charge as that of ACE.
> Moreover that charge must be set to 0.5973 for C, and -0.5679 for O.
> The same criteria should be applied to the N-H of the aminoacid and
> that of NMA.
>
> I have read the RED manual but it does not have information about doing
> this. I think that I could solve the problem using directly RESP, but
> this is probable more difficult. I am reading the file resp.doc but it
> has a lot of variables I donīt understand. Please if you can tell me
> what to do, I will be very grateful.

You cannot do it directly, you have to manually modify the inputs generated by
R.E.D. (in a second time) after running R.E.D. without restraint:
See http://structbio.vanderbilt.edu/archives/amber-archive/2004/1516.phtml
You have all what you need.

Regards, Francois

PS
I need to summarize FAQ related to R.E.D. on the R.E.D. web site

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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