Dear Sir,
I am running the NMODE analysis calculation on protein and
ligand for entropy calculation. My total data set is 20ns out of which
we use 4ns trajectory
with 50ps interval for enthalpy (dH) whereas last 1ns trajectory for
entropy calculation. for enthalpy it gives good result but for the
entropy it runs for
longer time and ends with the error in complex.out file
here, I use this command line for paralle run.
$AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS_MMPBSA.dat -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y nmode.mdcrd >
progress.log
The mmpbsa.in input file is
Input file for running GB
&general
startframe=1, endframe=100,
interval=2, keep_files=0, verbose=1,
/
&nmode
nmstartframe=1, nmendframe=100,
nminterval=2, nmode_igb=1, nmode_istrng=0.1,
maxcyc=5000, drms=0.0001,
/
the output file with the error
_MMPBSA_complex_nm.out.0
LS: step= 1 it= 1
MIN: Iter = 286 NFunc = 9050 E = -5484.90534 RMSG = 1.0157360e-04
CG: It= 50 ( 0.941)q :-(
LS: i= 1 lhs_f= -1.0421998e-05 rhs_f= -2.1235288e-09
lhs_g= 3.5947439e-10 rhs_g= 1.9111759e-05
LS: step= 1 it= 1
MIN: Iter = 287 NFunc = 9101 E = -5484.90535 RMSG = 9.5231781e-05
----------------------------------------------------------------
END: :-) E = -5484.90535 RMSG = 0.0000952
----Convergence Satisfied----
> allocation failure in vector: nh = 1632725649
These allocation failure error i couldn't resolve.
Even though I change the maxcyc number upto 200 it doesn't work
(test file for entropy calculation running well
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm)
Thanking you
Bajarang
--
*Dr. Bajarang V. Kumbhar* M.Sc.
Ph.D
Post-Doctoral Fellow
Biophysics and Computational Biology,
Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai Mumbai-400076
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Received on Tue Apr 28 2015 - 04:30:03 PDT
