Hi Ray,
I have solved this problem by using MPICH-3.1.4. I recommend that you can test MMPBSA calculation by MMPBSA.py first.
Regards,
Lei
> 在 2019年8月17日，下午9:21，rluo.uci.edu 写道：
>
>
> Lei,
> Can you email me a test case , off the list, for me to take a look?
> All the best,
> Ray Luo, Ph.D.
> rayluo.rayluolab.org
>
> -------- Original Message --------
> Subject: Re: [AMBER] Error in MMPBSA calculation
> From: jacky zhao
> To: amber
> CC:
>
> Actually, I have found this error again. Our previous trajectory can be
> calculated by MMPBSA.py.MPI without any problem in previous version of
> amber18. Recently, I have updated to the latest version of amber18 and
> amber19. This error can be encountered.
> Anyone can help me?
> Thank you very much.
> Regards,
> Lei
>> å¨ 2019å¹´8æ16æ¥ï¼ä¸å4:14ï¼shivangi agarwal
> <shiviagarwalpharma.gmail.com> åéï¼
>>
>> Hello all
>>
>> I want to calculate MMGBSA from dcd file. I have converted it to .mdcrd
>> using cpptraj.
>>
>> cpptraj -p complex-box.prmtop -y sim1_14.dcd -x sim1_14_complex.mdcrd
>> Then using,
>>
>> MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_20_frames.dat -sp
>> complex-box.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop
>> -y sim1_14_complex.mdcrd
>>
>> ###MMPBSA.in#############
>>
>> Input file for running PB and GB in serial
>> &general
>> endframe=20, keep_files=2,
>> /
>> &gb
>> igb=2, saltcon=0.100,
>> /
>> &pb
>> istrng=0.100,
>> /
>> ################################
>>
>> But getting error,
>>
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> mmpbsa_py_energy found! Using
> /opt/apps/amber/amber12/bin/mmpbsa_py_energy
>> cpptraj found! Using /opt/apps/amber/amber12/bin/cpptraj
>> Preparing trajectories for simulation...
>> 20 frames were processed by cpptraj for use in calculation.
>>
>> Beginning GB calculations with
> /opt/apps/amber/amber12/bin/mmpbsa_py_energy
>> calculating complex contribution...
>> calculating receptor contribution...
>> calculating ligand contribution...
>>
>> Beginning PB calculations with
> /opt/apps/amber/amber12/bin/mmpbsa_py_energy
>> calculating complex contribution...
>> CalcError: /opt/apps/amber/amber12/bin/mmpbsa_py_energy failed with
> prmtop
>> complex.prmtop!
>> Exiting. All files have been retained.
>>
>> Can someone suggest?
>>
>> Regards
>> Shivangi Agarwal
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Received on Sat Aug 17 2019 - 20:00:02 PDT
