Hi Ula!
You may want to try adding the following NMODE parameters in your mmpbsa input file.
.NM
PROC 2
MAXCYC 10000
DRMS 0.5
IGB 0
SALTCON 0.00
EXTDIEL 80.0
SURFTEN 0.0072
DIELC 4
Jenk
________________________________
From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, January 18, 2012 1:42 PM
Subject: [AMBER] nmode error
Dear Amber users
I make a MM_PB/GBSA analysis of a protein ligand complex. I performed a
calculation without normal mode analysis and it worked fine. But if i use the
same input file and switch nmode to 1 i get the error
Checking sanity
Checking GENERAL
Checking NM
Param PROC does not exist
Input file:
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
.GENERAL
#
# NM - Calculation of entropies with nmode.
#
VERBOSE 0
PARALLEL 0
#
PREFIX L
PATH ./
START 1
STOP 1
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
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
#
################################################################################
#
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
#
################################################################################
.PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################
What is the problem here?
best reagrds
Urszula
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Received on Wed Jan 18 2012 - 05:30:02 PST
