I check my seventh pdb file of complex in xleap.It seems that there is no superposition of atoms and only several warnings about close contact of 1.4XXXXX angstroms between XXX and XXX.
Using the same input files including prmtop files and inpcrd files of my ligand and receptor and complex, the binding free energy can be calculated by MMPBSA.py.
At 2016-04-14 19:45:32, "David A Case" <david.case.rutgers.edu> wrote:
>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 - 19:30:06 PDT
