AMBER Archive (2006)

Subject: Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI”

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Apr 24 2006 - 13:40:28 CDT

Since Amber developers know very little about Delphi, you're encouraged
to use PBSA for your mmpbsa jobs. If you have any problem with PBSA, we
will be able to help you. The two programs agree within1% given
identical parameters and conditions.

haixiao jin wrote:

> The system contains protein, ATP, MG.
>
> I want to calculate the binding energy between ATP and protein.
>
> 1. com.pdb (protein, ATP, two MG)
>
> receptor.pdb (protein, two MG)
>
> ATP.pdb (ATP)
>
> The parameter of ATP was added in xleap
>
> 2. dephi.crg file revised.
>
> The charge of C terminal and N –terminal residue was changed
>
> The charge of ATP was addedl
>
> 3. atmtypenumber file revised
>
> the atom type of atom in ATP was added according to the atom type of
> atom in GTP
>
>
>
> to get out snapshot of trajectory has run well, without any error
> message, but calculated the binding energy could not run, with this
> message : "Found unknown atflag DELPHI". Why?
>
> What do I do next? Thank you for help in advance!
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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