AMBER Archive (2003)

Subject: Re: No statistical output for MM-PBSA?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Apr 16 2003 - 13:05:38 CDT

Hi,

> Hi:
> I try to decompose the interaction energy between a ligand and some water
> molecules. I did the same thing done in the example of MM-PBSA in amber
> package. Finally I got the energies, but the program is stopped when getting to
> statistical part. This is the error I get:
> Reading files
> Reading dhnp-crd_com.all.out
> Reading dhnp-crd_rec.all.out
> Checking CALC
> Argument " Missing SINT for MM in 0+1 (residue 1216" isn't numeric in
> addition (+) at /opt/programs/amber7/src/mm_pbsa/
> mm_pbsa_statistics.pm line 1482, <IN> line 3653.

Could you send me your dhnp-crd_XXX.all.out files together with the
mm_pbsa.in file?

> Any hint? Please help me. Another question is I run MD for the ligand with
> thousands of water molecules, if I just want to get the interaction energy
> between the ligand and the whole solvent, is there an easy way to do that since
> those energies for each water molecule are not useful for me? Because it takes
> a long time to calculate that.

>From a practical point of view, you could use the ligand as ligand, the
surrounding water molecules as receptor (i.e. separate the coordinates
of both), and the ligand inside the solvent as complex. Then you calc a
"complex formation" between ligand and "receptor" to get the interaction
energy between both. But I'm not really sure what you want to use this
number for?

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++