Re: [AMBER] MMPBSA is not performing

From: <asma.msbi28.iiu.edu.pk>
Date: Tue, 08 Sep 2015 17:07:23 +0500

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
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Received on Tue Sep 08 2015 - 05:30:04 PDT
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