Many thanks, I'm trying with the ligand and receptor masks. Actually I am doing it for the first time and was seeing how it works so that i may have some know how of how it works.
Best regards,
Asma
Sent from my BlackBerry 10 smartphone.
Original Message
From: Aleksandra Skoric
Sent: Tuesday, 8 September 2015 13:30
To: AMBER Mailing List
Reply To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA is not performing
Dear Asma,
Well, it is not normal...
I would say that your input 'mmpbsa.in' is too general.
For instance, in &general namelist you don't have either ligand_mask or
receptor_mask, thus it could be that best guess for your receptor and
ligand is actually the worst one. :)
Try to define what is receptor and what is ligand in your complex and see
what happens.
Sandra
On Tue, Sep 8, 2015 at 10:08 AM, <asma.msbi28.iiu.edu.pk> wrote:
> Dear Sandra,
>
> Thanks for pointing it out. I was trying before with alanine _ scanning
> namelist and have now again ran the job with modified mmpbsa.in file
> including the alanine scanning namelist, but in every case my problem is
> same.
>
> I was just noticing the files generated by mmpbsa.py command and the _
> MMPBSA_complex.pdb file is incomplete, it has just three atoms from ligand
> and even the coordinates in the last line are not complete...is this
> normal?
>
> Best regards,
> Asma
>
> Sent from my BlackBerry 10 smartphone.
> Original Message
> From: Aleksandra Skoric
> Sent: Tuesday, 8 September 2015 12:59
> To: AMBER Mailing List
> Reply To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA is not performing
>
> Dear Asma,
>
> Since you have -mc and -mr flags I suppose you want to do alannine
> scanning?
>
> However, in your mmpbsa.in there is no &alanine_scanning namelist, which
> is
> necessary for alanine scanning initialization.
>
> Please read
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section3.htm
>
>
> Sandra
>
> On Tue, Sep 8, 2015 at 9:21 AM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
> > Thanks for the suggestion.
> > I am still facing the same situation unfortunately.
> > Can you please suggest something else?
> >
> > Best regards,
> > Asma
> >
> > On Mon, Sep 7, 2015 at 5:31 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Mon, Sep 7, 2015 at 1:03 AM, Asma Abro 28-FBAS/MSBI/F09 <
> > > asma.msbi28.iiu.edu.pk> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I am trying to perform MMPBSA using Ambertools 12. All the files seem
> > > okay
> > > > but no progress is being observed ahead of this:
> > > >
> > >
> > > The first suggestion is to try updating to the latest version of
> > > AmberTools (version 15, freely available on http://ambermd.org) and
> see
> > if
> > > you experience the same problems.
> > >
> > > AmberTools 12 is now at least 3 years old, and there have been a number
> > of
> > > improvements released since then.
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > > _______________________________________________
> > > 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
> >
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Received on Tue Sep 08 2015 - 02:00:04 PDT
