Hi Hayden,
Here are my comments:
Example input from amber (adjusted to fit my system for parm and crd files
only):
*****************************************************************
.GENERAL
PREFIX snapshot
PATH ./
# I USUALLY REMOVE # FOR SIMPLICITY
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./HBD1_2SU.parm
RECPT ./HBD1.parm
LIGPT ./2SU.parm
#
GC 0
AS 0
DC 0
#
MM 0
&MM PLEASE TRY NOT TO MIX UP PARAMETERS FROM DIFFERENT SUBSETS. REMOVE THIS LINE. (I WOULD ALSO USE .MM NOT &MM)
DIELC 1.0 AGAIN REMOVE THIS LINE
GB 0
PB 0
MS 0
#
NM 1
#
.NM
DIELC 4
MAXCYC 1000
DRMS 0.1
My input file:
**********************************************************
.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 0
GB 0
PB 0
MS 0
NM 1
I USUALLY DO NOT PLACE A SPACE IN BETWEEN PARAMETERS FOR SIMPLICITY REASONS
.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
.NM YOUR .NM SUBSET PARAMETERS SEEM FINE
DIELEC 4
MAXCYC 100000
DRMS 0.0001
SAME HERE
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
SAME HERE
.MS
PROBE 0.0
OK . HERE IS AN INPUT FILE THAT YOU MAY TRY IN YOUR NEXT MM-PBSA EXPERIMENT.
.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
.NM
DIELEC 4
MAXCYC 100000
DRMS 0.0001
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.MM
DIELEC 1
AND PLEASE TRY NOT TO MIX-UP PARAMETERS IN DIFFERENT SUBSETS.
hope this helps.
regards,
jenk.
Hayden Eastwood <s0237717.sms.ed.ac.uk> wrote:
Dear Cenk
The error message was obtained regardless of whether I used the test file
examples (amber9/src/mm-pbsa/Examples/04_MMPBSA_Nmode/mm_pbsa.in) or my own
input file. In both cases I get a crash when both NM and MM = 1). The
appended input files were used and I varied the values of NM and MM in each
one.
Many thanks for your help
hayden
Example input from amber (adjusted to fit my system for parm and crd files
only):
*****************************************************************8
.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 0
&MM
DIELC 1.0
GB 0
PB 0
MS 0
#
NM 1
#
.NM
DIELC 4
MAXCYC 1000
DRMS 0.1
**********************************************************
My input file:
**********************************************************
.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 0
GB 0
PB 0
MS 0
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
.NM
DIELEC 4
MAXCYC 100000
DRMS 0.0001
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
---------------------------------
Ahhh...imagining that irresistible "new car" smell?
Check outnew cars at Yahoo! Autos.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 06 2007 - 06:07:06 PDT
