From the cmd line:
/home/programs/amber/amber14/bin/sander -O -i pbsa_com.in -o pbsa_com.7.out -c ./snapshot_com.crd.7 -p ./com.prmtop
You are getting energy errors that might indicate a superposition of atoms.
What does snapshot_com.crd.7 look like? Is it corrupted in some way?
Bill
On 4/14/16 12:42 AM, yhzahsc wrote:
> Dear Experts,
> 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
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> /home/programs/amber/amber14/bin/sander -O -i pbsa_com.in -o pbsa_com.7.out -c ./snapshot_com.crd.7 -p ./com.prmtop not successful
> For details see: http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
>
>
> I followed the indications to search for 'http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful'.I did not find the error mentioned in the webpage in my 'pbsa_com.7.out' but errors as following:
>
>
> 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
>
> Could you please suggest me how to solve this problem?
>
>
> Thanks in advance.
> yhz
>
>
>
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Received on Thu Apr 14 2016 - 02:00:04 PDT
