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
Received on Mon Sep 02 2019 - 00:00:03 PDT
