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

From: Ravi Abrol <raviabrol.gmail.com> Date: Sun, 20 Feb 2022 15:15:11 -0800

---
On Sun, Feb 20, 2022 at 8:30 AM Ray Luo <rluo.uci.edu> wrote:
> Hi Ravi,
>
> One of the mmpbsa.py test cases in the $AMBERHOME/AmberTools/test directory
> is for membrane proteins. You can use it for your initial setup. However,
> the PB decomposition doesn't work for membrane proteins.
>
> All the best,
> Ray
> --
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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