The MMPBSA.py script is consistently crashing while analyzing
_MMPBSA_complex_gb.mdout. The following is written in the .mdout
Reading parm file (com.top)
title:
mm_options: e_debug=2
mm_options: gb=2
mm_options: rgbmax=25.000000
mm_options: gbsa=1
mm_options: surften=0.007200
mm_options: cut=999.000000
mm_options: epsext=78.300000
mm_options: kappa=0.103952
bad number of bonds to C: 3044 1; using default carbon parameters
bad number of bonds to C: 3051 1; using default carbon parameters
bad number of bonds to C: 3055 1; using default carbon parameters
Processing ASCII trajectory (_MMPBSA_complex.mdcrd)
Processing frame 1
iter Total bad vdW elect nonpolar genBorn
frms
eff.c(3678) enb14 --> 1951.115
eff.c(3679) eel14 --> 18106.965
eff.c(3737) enb --> -4318.441
eff.c(3738) eel --> -35895.304
eff.c(3739) e_gb --> -4932.438
eff.c(3740) esurf --> 177.234
eff.c(3741) evdwnp --> 0.000
ff: 0 -13689.29 11221.58 -2367.33 -17788.34 177.23 -4932.44
1.81e+01
The job got crashed after processing 1st frame.
In VMD I have visualized _MMPBSA_complex.pdb, the atoms 3044, 3051, and 3055
are not bonded to C atom. Why it is showing this error?
Thanks,
mani
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Received on Tue Jul 12 2011 - 13:30:03 PDT
