On Thu, Apr 14, 2016, yhzahsc wrote:
> I am trying to use mm_pbsa.pl to calculate binding free energy between
> a protein and RNA.The length of trajectory is 30ns. I selected about 31
> snapshots from the beginning to the end. The program always stopped in
> the middle of the procedure and the outfile 'binding_energy.log' gave
> the errors:
>
>
> Calc contrib for ./snapshot_com.crd.7
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 1.3733E+07 O 8437
>
>
> BOND = ************* ANGLE = 1406040.6688 DIHED = 44721.8728
> VDWAALS = NaN EEL = +Infinity EPB = -56004.1098
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
> ECAVITY = 311026.9588 EDISPER = 0.0000
>
It looks like snapshot 7 is corrupted somehow. Have you visualized this
structure, and compared it to others before and after it?
...dac
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Received on Thu Apr 14 2016 - 05:00:03 PDT
