AMBER Archive (2008)

Subject: AMBER: Error- MM_PBSA calculation

From: vikky 99 (vsaivikram_at_gmail.com)
Date: Thu Mar 27 2008 - 03:47:53 CDT

Dear all,

I am calculating free binding energy for a complex system that has protein
and a small ligand, by using MM_PBSA module in amber9 . As given in
tutorial, foremost made an input to generate snapshots for Complex,
Receptor and ligand. The job was successful and i got snapshots but all are
empty.

 Here is the Input:

GENERAL
 PREFIX snapshot
 PATH ../
 COMPLEX 1
 RECEPTOR 1
 LIGAND 1
 COMPT ../_com.top
 RECPT ../_rec.top
 LIGPT ../_lig.top
 GC 1
 AS 0
 DC 0
 MM 0
 GB 0
 PB 0
 MS 0
 NM 0
@MAKECRD
BOX YES
NTOTAL 77135
NSTART 1
NSTOP 100
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 9487
LSTOP 9546
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 9486
@TRAJECTORY
TRAJECTORY ./md1.crd
@PROGRAMS

 Along with the empty snapshot files MM_PBSA generated three additional
files with the names (fort.10, fort.11, and fort.12) which are having the
last set of coordinates for Commplex, Receptor and Ligand respectively. I
would like to know What are those files?

 Help me to solve it.

-Live life on your own terms-
Varsha rani

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