Dear Sandra,
Many thanks. I'll do it with the file you suggested and will see if it works.
Best regards,
Asma
Sent from my BlackBerry 10 smartphone.
Original Message
From: Aleksandra Skoric
Sent: Tuesday, 8 September 2015 16:00
To: AMBER Mailing List
Reply To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA is not performing
Dear Asma,
First, let's reduce the number of unknowns.
Make your input file without &alanine_scanning and &pb
input file would be:
&general
startframe=1, endframe=50, interval=1,
receptor_mask=:1-327, ligand_mask=:328,
verbose=1,
/
&gb
saltcon=0.1,
/
And then issue this command:
/home/AAData/AMBER/amber14/bin/MMPBSA.py -O -i mmpbsa.in -o mmgbsa.dat -sp
sam-as3mt-sol.top -cp sam-as3mt.top -rp AS3MT.top -lp sam.top -y
sam-as3mtprod9.mdcrd
(without -mc and -mr flags)
And again see what happens. :)
Sandra
On Tue, Sep 8, 2015 at 12:02 PM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> Yes you are right, all I am getting is:
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/AAData/AMBER/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /home/AAData/AMBER/amber14/bin/cpptraj
> Preparing trajectories for simulation...
>
> I have added comma as well but no difference. I think I must be missing
> something else or making a mistake somewhere else but unable to point my
> finger to that..
>
> Best Regards,
> Asma
>
> On Tue, Sep 8, 2015 at 2:46 PM, Aleksandra Skoric <
> skoricaleksandra.gmail.com> wrote:
>
> > All you get when you issue this command:
> >
> >
> > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp sam-as3mt-sol.top -cp
> > sam-as3mt.top -rp AS3MT.top -lp sam.top -y sam-as3mtprod9.mdcrd -mc
> > as3mt-sam-mut1.top -mr as3mt-mut1.top
> >
> > is:
> >
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> > /home/student/Working/amber12/
> > cpptraj found! Using /home/student/Working/amber12/
> > Preparing trajectories for simulation... ?
> >
> >
> > Anyhow, first put comma after ligand_mask=:328
> >
> > See what happens and then write again.
> >
> > Sandra
> >
> > On Tue, Sep 8, 2015 at 11:13 AM, Asma Abro 28-FBAS/MSBI/F09 <
> > asma.msbi28.iiu.edu.pk> wrote:
> >
> > > 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
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> > > > > > >
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Received on Tue Sep 08 2015 - 05:30:04 PDT
