Dear Amber users,
I am using MM_PBSA module in amber9 for calculating the Free binding energy
of a complex (Protein + Inhibitor). At first i am generating snapshots for
three systems, Complex, Receptor and ligand, from the entire trajectory. I
managed to get the snapshots but all are empty when i tried to open them.
Input:
GENERAL
PREFIX snapshot
PATH ../
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ../_complex.top
RECPT ../_receptor.top
LIGPT ../_ligand.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 10
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 9487
LSTOP 9546
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 9486
.TRAJECTORY
TRAJECTORY ../md1.crd
TRAJECTORY ../md2.crd
TRAJECTORY ../md3.crd
.PROGRAMS
Kindly some one suggests me how to solve it.
Thanks in advance.
Sai vikrama chaitanya. V
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Received on Sun Oct 14 2007 - 06:07:19 PDT
