Hi
If you see the tutorial in
http://ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm,
They use the example of the protein-protein complex (Ras-Raf).
Best Regards
On Mon, 2 Sep 2019 at 12:27, maryam azimzadehirani <maryamai1988.gmail.com>
wrote:
> Thanks for your reply, but I do get errors in this case. To be precise: I
> can successfully run the analysis when a small (50 a.a) ligand is bound to
> this protein. Once I run the same analysis for the simulations of the same
> receptor bound to a large ligand (300 a.a), I get the error that the
> ligand.gb.surf file was not written by the program:
> IOError: [Errno 2] No such file or directory:
> '_MMPBSA_ligand_gb_surf.dat.0'
>
> I have posted this issue last week:
> http://archive.ambermd.org/201908/0291.html
>
> The simulations are fine, the parm/top files are fine, as that I can load
> them in vmd and do any other sort of analysis with AMBER tools without
> arguments. I am not sure what is going wrong here.
> thanks,
>
>
> On Mon, Sep 2, 2019 at 11:12 AM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Hello
> > It should not matter, as MMGBSA can be used to compute binding energy for
> > protein-protein complex.
> > Best Regards
> >
> >
> >
> > On Mon, 2 Sep 2019 at 11:29, maryam azimzadehirani <
> maryamai1988.gmail.com
> > >
> > wrote:
> >
> > > Deal all,
> > > does the size of ligand matter in running MMGBSA.py analysis? Meaning
> if
> > > the ligand and receptor are two protein chains of relatively same
> length,
> > > this could cause an error?
> > >
> > > *Maryam Azimzadeh Irani *
> > >
> > >
> > > *PhD in Computational Structural Biology *
> > > _______________________________________________
> > > 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
> >
>
>
> --
>
> *Maryam Azimzadeh Irani *
>
>
> *PhD in Computational Structural Biology *
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 02 2019 - 00:30:02 PDT
