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 16:44:49, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> 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 - 19:30:05 PDT
