Dear Amber users,
I am trying to run NM calculations, but i am getting an error:
/lap/amber/11.0.17_AT1.5/bin/nmode -O -i nmode_com.in -o nmode_com.1.out -c sanmin_com.1.restrt -p ./COM.prmtop not running properly
For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_NM_entropy_not_running_properly
inside the nmode_com.1.out I have
PARM file has the title:
S56
Total memory required : 934033531 real words
Total memory required : 35117277 integer words
Total memory required : 25489 4-character words
Maximum nonbond pairs 34573769
ASSERTion ' ier == 0 ' failed in nmode.f at line 114.
whta does that mean?
input file that i am using:
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
#
VERBOSE 0
PARALLEL 0
#
PREFIX L
PATH ./
START 1
STOP 10
OFFSET 1
#
COMPLEX 1
RECEPTOR 0
LIGAND 0
#
COMPT ./COM.prmtop
RECPT ./REC.prmtop
LIGPT ./LIG.prmtop
#
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
INP 1
#
SURFTEN 0.04356
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
# The following parameters are passed to sander.
# For further details see the sander documentation.
#
# DIELC - Dielectricity constant for electrostatic interactions.
# Note: This is not related to GB calculations.
#
DIELC 1.0
#
################################################################################
.GB
#
# GB parameters (this section is only relevant if GB = 1 above)
#
# The first group of the following parameters are passed to sander.
# For further details see the sander documentation.
#
# IGB - Switches between Tsui's GB (1) and Onufriev's GB (2, 5).
# GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
# Decomposition only works with ICOSA.
# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
# EXTDIEL - Dielectricity constant for the solvent.
# INTDIEL - Dielectricity constant for the solute.
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
IGB 5
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# In general, since Bondi radii are already augmented by 1.4A,
# PROBE should be 0.0
# In IVCAP = 1 or 5, the solvent excluded surface is required for
# calculating the cavity contribution. Bondi radii are not
# augmented in this case and PROBE should be 1.4.
#
PROBE 0.0
#
################################################################################
.NM
PROC 2
MAXCYC 10000
DRMS 0.5
IGB 0
DIELC 4
#
#################################################################################
/Urszula
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Received on Sun Feb 05 2012 - 13:00:02 PST
