Re: [AMBER] MMPBSA.py for membrane proteins with per-residue decomposition

From: Ray Luo <rluo.uci.edu> Date: Sun, 20 Feb 2022 08:29:42 -0800

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Feb 18, 2022 at 8:17 PM Ravi Abrol <raviabrol.gmail.com> wrote:
> Hi,
>
> I am trying to run MMPBSA.py with -make-mdins flag so that I can modify the
> mdin files for use with membrane proteins and also carry out the
> per-residue decomposition. I am using the following input file:
>
> Input file for PB calculation MMPBSA with membrane proteins from the manual
> with recommended parameters like ipb=1:
> <<<
> &general
>    use_sander=1,
>    startframe=1, endframe=5, interval=1,
>    keep_files=2, netcdf=1, debug_printlevel=2
> /
> &pb
>  istrng=0.150, bcopt=10, fillratio=1.5,
>  mthick=36.8555, mctrdz=0, indi=2.0,
>  eneopt=1, nfocus=1, inp=1, cutfd=7.0, cutnb=99.0,
>  ipb=1, npbverb=1, solvopt=2, radiopt=0,
>  maxarcdot=15000, poretype=0,
>  memopt=1,
> /
> &decomp
>  dec_verbose=3, idecomp=2,
> /
> >>>
> but MMPBSA.py with -make-mdins flag gets rid of memopt option and other
> options from the original &pb section and also sets ipb=2. It produces
> three mdin files (complex, receptor, ligand). Here is the complex input
> file produced: _MMPBSA_pb_decomp_com.mdin
> <<<
> File generated by MMPBSA.py
> &cntrl
>  ntb=0, nsnb=99999, cut=999.0,
>  ioutfm=1, imin=5, igb=10, idecomp=2,
>  ipb=2, inp=1,
> /
> &pb
>  epsin=2.0, istrng=150.0, radiopt=0,
>  maxitn=1000, fillratio=1.5,
> /
> Residues considered as REC
> RRES 1 468
> END
> Residues considered as LIG
> LRES 469 683
> END
> Residues to print
> RES 1 683
> END
> END
> >>>
>
> If I don't include the &decomp section in the original input file, then
> the -make-mdins flag produces two input files *mdin and *mdin2 and but this
> time respects the memopt flag.
>
> Should one assume that per-residue decomposition is not implemented yet
> with memopt=1,2,3 and for membrane proteins?
>
> If it is, can I add the &pb section parameters I need for membrane proteins
> back into the three mdin files (complex, receptor, ligand)?
>
> Also, will the three mdin files (complex, receptor, ligand) files be all I
> would need to change?
>
> Thanks,
> Ravi
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