AMBER Archive (2003)

Subject: Re: no statistics.out in mm_pbsa binding energy calculations

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Feb 19 2003 - 12:48:59 CST

Hi,

how does your all.out files look like? Do you find values for all the
energy contributions (MM, GB, PB, MS) you asked for? If not, have a look
at the calc_MM_GB_SAS, calc_PB, and calc_ms functions. Comment the lines
"unlink $sanout", "unlink $delphiout", "unlink $mol", resp., and rerun
mm_pbsa for a few of your snapshots. Then you should get the output
files of the single programs, which might give you a better hint what
fails.

Best regards

Holger

> Hi, I have generated the snapshots sucessfully. When I
> calculate the binding energy, I get three all.out
> files for inhibitor,receptor and the complex properly.
> However there is no statistics.out file. The log file
> shows the following message:
> No values for MM_GAS existing -> Skipping
> No values for PB_PBSOL existing -> Skipping
>
> Thanks.
> Eric
>
> Here is part of the mm_pbsa.in.
> PREFIX 4TS
> PATH snapshots/
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../4bound.top
> RECPT ../4protein.top
> LIGPT ../4TS.top
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++++++++++