Dear Sandra,
Now I am giving this input file:
sample input file
&general
startframe=1, endframe=50, interval=1,
receptor_mask=:1-327, ligand_mask=:328
verbose=1,
/
&gb
saltcon=0.1
/
&pb
istrng=0.100
/
&alanine_scanning
/
And still the files are same. No improvement in results. Can you please
suggest something else?
Many thanks and best regards,
Asma
On Tue, Sep 8, 2015 at 1:35 PM, <asma.msbi28.iiu.edu.pk> wrote:
> 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
> > > >
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> > >
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> >
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> >
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Received on Tue Sep 08 2015 - 02:30:03 PDT
