I am running some simulations of a small molecule I have docked to a protein using autodock vina. I ran the small molecule through antechamber, leap etc without any problems. I then wished to do the preparatory equilibration runs as in the MMPBSA tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/section1.htm)
when I get to the heating section- as seen using VMD- all the bonds in the entire system become distorted/lengthened. The only error message I get is:
mpirun -np 8 pmemd.MPI -O -i min.in -o min.out -p 2psj_2dab_11413.prmtop -c 2psj_2dab_11413.inpcrd -r 2psj_2dab_11413_min.rst -ref 2psj_2dab_11413.inpcrd
mpirun -np 8 pmemd.MPI -O -i heat.in -o 2psj_2dab_11413_heat.out -p 2psj_2dab_11413.prmtop -c 2psj_2dab_11413_min.rst -r 2psj_2dab_11413_heat.rst -x 2psj_2dab_11413_heat.mdcrd -ref 2psj_2dab_11413_min.rst
vlimit exceeded for step 16569; vmax = 29.8253
vlimit exceeded for step 16570; vmax = 60.3048
furthermore, in the min.out file, I see the error message:
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -1.1054E+05 1.3305E+01 4.0749E+01 O 37429
BOND = 185.6023 ANGLE = 916.6475 DIHED = 3027.8768
VDWAALS = 4237.6018 EEL = -134189.6440 HBOND = 0.0000
1-4 VDW = 1053.9021 1-4 EEL = 14180.0909 RESTRAINT = 47.5156
EAMBER = -110587.9227
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
614 -1.1054E+05 1.3305E+01 4.0749E+01 O 37429
BOND = 185.6023 ANGLE = 916.6474 DIHED = 3027.8767
VDWAALS = 4237.6014 EEL = -134189.6431 HBOND = 0.0000
1-4 VDW = 1053.9021 1-4 EEL = 14180.0909 RESTRAINT = 47.5156
EAMBER = -110587.9222
***** REPEATED LINMIN FAILURE *****
What could be wrong here? I realize this isn't much information to go on.
Turning SHAKE off doesn't fix the problem
Thanks for any help
Chris
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Received on Mon Jan 14 2013 - 15:30:03 PST
