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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Received on Fri Apr 18 2008 - 21:14:22 PDT
