Dear all,
I want to run conventional MD simulation on a protein complex with a small molecule. But it has been broken in the first step. The .in and .out file are shown below. I am wondering what is the problem and how to explain it. I appreciate any help from you:)
Initial minimisation with Cartesian restrains for the solvent (hold the protein and Cl-)
&cntrl
imin=1, maxcyc=3000,
ntr=1,
restraint_wt=100,
restraintmask=':1-90'
&end
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.3472E+08 2.4011E+02 1.9793E+04 C 1441
BOND = 9784.2491 ANGLE = 1786.4015 DIHED = 934.9579
VDWAALS = ************* EEL = -62579.0562 HBOND = 0.0000
1-4 VDW = 1083.6816 1-4 EEL = 4202.4250 RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -8.3706E+09 8.5391E+04 8.3864E+06 C5 1446
BOND = 12553.8921 ANGLE = 2862.0259 DIHED = 952.0556
VDWAALS = ************* EEL = -64213.1361 HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 4191.5379 RESTRAINT = 3088.1670
EAMBER = *************
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
68 -8.3706E+09 8.5391E+04 8.3864E+06 C5 1446
BOND = 12554.0865 ANGLE = 2862.0342 DIHED = 952.0557
VDWAALS = ************* EEL = -64213.1344 HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 4191.5380 RESTRAINT = 3088.1696
EAMBER = *************
***** REPEATED LINMIN FAILURE *****
Thank you very much in advance and kind regards,
Zhonghua
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Received on Fri Mar 08 2019 - 01:30:02 PST
