Hi All,
I am using MMPBSA script in serial, of AmberTools1.5 for entropy
calculations. I have successfully calculated PBSA and GBSA for the complex
system. But when I am performing nab calculations it is giving following
error in the progress.log
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Warning: RADIUS_SET cannot be found in your prmtop files!
ptraj found! Using /home/srg/mhb75/Download/amber11/bin/ptraj
nmode program found! Using
/home/srg/mhb75/Download/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
1 frames were read in and processed by ptraj for use in calculation.
Beginning nmode calculations with mmpbsa_py_nabnmode...
Calculating normal modes for 1 frames
calculating complex contribution for frame 0
sh: line 1: 27098 Killed
/home/srg/mhb75/Download/amber11/bin/mmpbsa_py_nabnmode
_MMPBSA_complex_nm.pdb.1 complex_nw.prmtop 10000 0.001 "ntpr=10000, diel=C,
kappa=0.103951911959, cut=1000, gb=1, dielc=4.0, temp0=298.15, wcons=0" >>
_MMPBSA_complex_nm.out
Error: error during mmpbsa_py_nabnmode calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
The script is getting crashed when the complex minization is done.
The _MMPBSA_complex_nm.out last lines looks like
LS: step= 1 it= 1
MIN: It= 280 nfunc= 8235 E= -3850.77578 ( 1.38e-03)
CG: It= 50 ( 1.018)q :-(
LS: i= 1 lhs_f= -0.0010710421 rhs_f= -2.1445542e-07
lhs_g= 2.8783911e-06 rhs_g= 0.0019300988
LS: step= 1 it= 1
MIN: It= 281 nfunc= 8286 E= -3850.77685 ( 1.29e-03)
CG: It= 50 ( 1.014)q :-(
LS: i= 1 lhs_f= -0.001007292 rhs_f= -2.0161816e-07
lhs_g= 1.6685223e-06 rhs_g= 0.0018145635
LS: step= 1 it= 1
MIN: It= 282 nfunc= 8337 E= -3850.77786 ( 1.19e-03)
CG: It= 50 ( 0.905)q :-(
LS: i= 1 lhs_f= -0.00081047998 rhs_f= -1.6216577e-07
lhs_g= 1.322888e-07 rhs_g= 0.0014594919
LS: step= 1 it= 1
MIN: It= 283 nfunc= 8388 E= -3850.77867 ( 9.95e-04)
----------------------------------------------------------------
FIN: :-) E= -3850.78 ( 0.001)
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn
frm
I am also performing nmode calculations for 50 snapshots for other systems
and they are working fine. But for the above system even for one snapshot
the script is getting crashed.
Thanks,
mani
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Received on Thu Aug 04 2011 - 09:30:04 PDT
