AMBER Archive (2003)

Subject: AMBER: MM_PBSA(GBSA) Examples

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Thu Sep 25 2003 - 10:56:23 CDT

Hi Kazuo:

When I tried to open your mm_pbsa_2.in attachment, it contained
a lot of extraneous ASCII - font directives and so forth. Perhaps that
is part of the problem.

Your attachment's PREFIX line refers to snapshot files that are not supplied
in the Example directories on our Amber 7 distribution here.

So, starting from the mm_pbsa.in file in my 03_MMBPSA_Binding directory, I
created a ligand-only input file with PB=0 to try to duplicate your errors:

@GENERAL
PREFIX ras_raf_II_wt
PATH ../01_GenerateSnapshots/
COMPLEX 0
RECEPTOR 0
LIGAND 1
COMPT ../ras_raf_II_wt.prmtop
RECPT ../ras_II_wt.prmtop
LIGPT ../raf_wt.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 0
MS 1
NM 0
@GB
IGB 4
SALTCON 0.00
EXTDIEL 80.0
SURFTEN 0.0072
SURFOFF 0.00

Running mm_pbsa with the above as the input file, from the 03_MMBPSA_Binding
directory gives me this statistics file at the end:

# MEAN STD
# =======================
ELE -2041.95 13.35
VDW -290.72 7.24
INT 1273.52 24.76
GAS -1059.15 22.28
GBSUR 31.38 0.12
GB -1638.92 10.98
GBSOL -1607.55 10.98
GBELE -3680.88 10.73
GBTOT -2666.69 22.79

I hope some of this is helpful. I am learning MM_PBSA myself - and look
forward to hearing the final solution.

Cheers

Chris

>===== Original Message From amber_at_scripps.edu =====
>Dear Dr. Holger Gohlke and Amber users;
>
> I have tried to run MM_PBSA(GBSA) Examples 03_MM_PBSA_Binding.
>Selecting only ligand and GB for the first time, I made the input file as
>attached.
>Run the mm_pbsa.pl, the log file stopped at the => Treat Special Parameters,
>saying "Can't use an undefined value as an Array reference at
>/usr/local/amber7/src/mm_pbsa/_statics.pm line 1234.
>I referred to AMBER Archive to find no suggestion.
>I would appreiciate it very much if you kindly tell me the solution.
>Sincerely Yours.
>Kazuo Koyano
>
>Center for Collaborative Research, The University of Tokyo
>4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
>Tel; 03-5452-6587 Fax; 03-5452-6545
>E-mail koyano_at_fsis.iis.u-tokyo.ac.jp

Chris Moth
chris.moth_at_vanderbilt.edu

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