the input command is similar for protein-protein and protein-ligand binding
energy calculations.
On Mon, Sep 2, 2019 at 11:31 AM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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
> >
> _______________________________________________
> 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
Received on Mon Sep 02 2019 - 00:30:02 PDT
