Dear Amber Users,
I am using mm_pbsa.pl version now and have a error message during
normal mode analysis.
After I generated snapshots from my MD simulations (Results are
stable), I could calculate PB and GB solvation energy with successful
energy decomposition.
However, when I tried to calculate entropy terms, nmode input files
indicated "ntx = 0".
Since my coordinate files are formated, calculation stops very
beginning.
Even when I set ntx = 1 in mm_pbsa input file as following, nmode
input files which are automatically generated by mm_pbsa.pl still have
ntx = 0.
.NM
#
# Parameters for sander/nmode calculation (this section is only
relevant if NM = 1 above)
#
# The following parameters are passed to sander (for minimization)
and nmode
# (for entropy calculation using gasphase statistical mechanics).
# For further details see documentation.
#
# DIELC - (Distance-dependent) dielectric constant
# MAXCYC - Maximum number of cycles of minimization.
# DRMS - Convergence criterion for the energy gradient.
#
DIELC 4
MAXCYC 1000
DRMS 0.1
NTX 1
#
Isn't default value of ntx for normal mode 1? I'm wondering if there
is a way I can make nmode input files have ntx as 1.
Thanks in advance,
Best regards,
Seungyeul Yoo, Ph.D Candidate
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
East Building, 16th floor, Room 16-34A
New York, NY 10029
+1 (212) 6595477
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Received on Tue May 18 2010 - 15:30:03 PDT
