Hi all,
I tried normal mode calculations in a protein (268 aa long). I used parallel
version of MMPBSA.py.MPI (python script) for calculating the entropy. The no
results written out in FINAL_RESULTS_MMPBSA.dat . following is the output,
can you please point the possible places where I am doing wrong. The _MMPBSA
_complex_nm.out and _MMPBSA_receptor_nm.out files contain an error
"allocation failure in vector: nh = 284339701 ", where as _MMPBSA_ligand_nm.out
doesnot have this error. This looks like an memory allocation problem but I
had also tried the calculations by assigning 8GB of memory and the problem
still persist. Can any of you point out teh origin of errors in the
calculations.
-----------------FINAL_RESULTS_MMPBSA.dat----------------
| Run on Tue Dec 14 02:33:44 CET 2010
|Input file:
|--------------------------------------------------------------
|Input file for running entropy calculations using NMode
|&general
| endframe=50, keep_files=2,
|/
|&nmode
|nmstartframe=5, nmendframe=45,
|nminterval=5, nmode_igb=1, nmode_istrng=0.1,
|/
|
|
|--------------------------------------------------------------
|Complex topology file: com.prmtop
|Receptor topology file: rec.prmtop
|Ligand topology file: lig.prmtop
|Initial mdcrd(s): prod.mdcrd
|
|Best guess for receptor mask: ":1-266"
|Best guess for ligand mask: ":267-268"
|Calculations performed using 50 frames.
|NMODE calculations performed using 9 frames.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
================== _MMPBSA_complex_nm.out
====================================
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn
frms
ff: 1 -1716.85 2410.88 -1792.90 -1732.53 0.00 -602.30
9.68e-04
Energy = -1.7168452022e+03
RMS gradient = 9.6806388713e-04
allocation failure in vector: nh = 280631737
Reading parm file (com.prmtop)
============================================================================
Thanking you in advance
.S
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Received on Tue Dec 14 2010 - 04:30:03 PST
