Dear David
Thanks for your reply.
My protein and ligand system contain 870 atoms (protein and ligand) so it
is might be due to large system.
regards
Bajarang
On Tue, Apr 28, 2015 at 4:36 PM, Bajarang Kumbhar <kumbharbajarang.gmail.com
> wrote:
> 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
>
--
*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 Wed May 06 2015 - 07:30:02 PDT
