Re: [AMBER] Error in MMPBSA calculation

From: Ray Luo <rluo.uci.edu>
Date: Fri, 16 Aug 2019 17:27:20 +0800

Hi Shivangi,

My guess is this is one of those errors due to the default radiopt=1
in the older amber releases ... Why not use amber18 or amber19
instead?

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Aug 16, 2019 at 4:23 PM shivangi agarwal
<shiviagarwalpharma.gmail.com> wrote:
>
> 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 Fri Aug 16 2019 - 02:30:02 PDT