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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 17 2019 - 06:30:02 PDT
