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
>
_______________________________________________
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
Received on Tue Sep 08 2015 - 01:30:02 PDT
