Dear all,
I am calculating free binding energy for a complex system, having protein
and a small ligand, by using MM_PBSA module in amber9 . As given in the
tutorial, foremost made an input to generate snapshots for three systems,
Complex, Receptor and ligand, from the entire trajectory that i got from
the simulation. The job went fine, as for i know, and it has generated the
snapshots but nothing has been found when i open them.
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 35000
NSTART 1
NSTOP 600
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 3256
LSTOP 3296
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3256
.TRAJECTORY
TRAJECTORY ../sim1.crd
TRAJECTORY ../sim2.crd
TRAJECTORY ../sim3.crd
.PROGRAMS
Help me to solve it.
-Live life on your own terms-
Varsha rani
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Received on Wed Oct 17 2007 - 06:07:39 PDT
