Dear amber:
The MMPBSA.pl was used to calculate the decomposing binding energy and the
input file was as following:
##################################################
.GENERAL
VERBOSE 0
PARALLEL 0
#
PREFIX wat
PATH ./
START 1
STOP 100
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./x-wat-com.prmtop
RECPT ./x-wat-pro.prmtop
LIGPT ./x-wat-lig.prmtop
#
GC 0
AS 0
DC 1
#
MM 1
GB 0
PB 1
MS 0
#
NM 0
#
.DECOMP
#
DCTYPE 2
#
COMREC 1-276
COMLIG 277-277
COMPRI 1-276 277-277
RECRES 1-276
RECPRI 1-276
RECMAP 1-276
LIGRES 1-1
LIGPRI 1-1
LIGMAP 277-277
#
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 56.97
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 1
INP 0
#
SURFTEN 0.04356
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
.MM
DIELC 1.0
#
.GB
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 56.97
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
.MS
PROBE 0.0
#
##############################################################
However, the file of statistics.out was not obtained in the end. And
then when we opened the files of com.all.out, rec.all.out, lig.all.out, all
of the values for PBSUR (the last column) were zero. Can you give me a hand
about this problem?
Thank you very much.
YANYAN ZHU
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Received on Wed Dec 25 2013 - 02:00:02 PST
