Step 1: close/overlapping vdw for 2+ atoms, the most prominent being C,
1441: look at that atom and its neighbors, especially nonbonded
neighbors, especially any atoms you supplied params for.
Step 50: Now 1-4 (bonded) vdw's are impacted. C5 1446 == in same
neighborhood, might be the 'other atom', assuming only two are tangoing,
as is usually the case.
On 3/8/19 1:18 AM, Zhonghua Xia wrote:
> 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 - 02:30:03 PST
