Dear Sir/Madam,
I was trying to do a MM-PBSA/GBSA calculation for the tutorial job. Since the PBSA cannot be done due to memory problem. I have to turn off the setting of PBSA but only allow to do the calculation for GBSA. Here is my input file modified from the tutorial input file. However, I found the energy calculated are extremely large, so, I am writing to ask if it is the proper procedure to turn off PBSA calculation when I am only interested to get GBSA binding energy? Did I do anything wrong in the following input file? Pls kindly help.
Thanks a lot.
=================================================================
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./ras-raf.prmtop
RECPT ./ras.prmtop
LIGPT ./raf.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 0
MS 1
NM 0
.PB
#PROC 2
#REFE 0
#INDI 1.0
#EXDI 80.0
#SCALE 2
#LINIT 1000
#PRBRAD 1.4
#ISTRNG 0.0
#RADIOPT 0
#NPOPT 1
#CAVITY_SURFTEN 0.0072
#CAVITY_OFFSET 0.00
#SURFTEN 0.0072
#SURFOFF 0.00
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.PROGRAMS
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Received on Fri Jul 09 2010 - 04:00:04 PDT
