In addition to other useful comments, you may also want to add the following parameters in your input.
.MM
DIELEC 1
.NM
DIELEC 4
MAXCYC 100000
DRMS 0.0001
you may also want to remove
.PROGRAMS
head in your input since you do not seem to need it.
Hope this helps,
jenk
Hayden Eastwood <s0237717.sms.ed.ac.uk> wrote: Dear Amber users
I'm running mm-pbsa on a small protein complex. When I run mm-pbsa with nm
set to 0, everything works fine. However, when I set nm = 1 so that I can
compute the entropy of the system the program crashes out whilst performing
the sanity check and gives me the following error message:
Param DIELC does not exist
My input file is as follows:
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./HBD1_2SU.parm
RECPT ./HBD1.parm
LIGPT ./2SU.parm
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 1
.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
.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
Any ideas as to how to get round the crash out?
Many thanks in advance
Hayden Eastwood
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Received on Wed May 02 2007 - 06:07:34 PDT
