Dear Jason and Sofia,
Many thanks for your opinions and suggestions.
I was guessing the same that the problem exist before it even goes for PB or GB calculations. However, I've ran the rmsd computation and there cpptraj is running fine.
I'll prepare the prmtop files and check again.
Best regards,
Asma
Sent from my BlackBerry 10 smartphone.
Original Message
From: Jason Swails
Sent: Tuesday, 8 September 2015 18:35
To: amber.ambermd.org
Reply To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA is not performing
On Tue, 2015-09-08 at 17:07 +0500, asma.msbi28.iiu.edu.pk wrote:
> 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,
I would actually suggest *against* specifying receptor_mask and
ligand_mask in your input file unless you *know* that the default
assignment is wrong or masks cannot be guessed (and the only way that
the guess would be wrong is if you had multiple copies of the ligand
bound to multiple active sites and you DIDN'T want the last ligand to be
treated as the "ligand"). The reason is that the default guesser serves
as a very useful consistency check for your topology files.
In this case, as long as your topology files are correct, then this will
be the mask guesses.
> > 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...
This is suggesting that the calculation is failing in the step of
creating the trajectories, which is done in the same way for every kind
of calculation. It doesn't even get to the GB or PB calculations, so
the problem exists before then.
Try processing your trajectory file with cpptraj separately from using
MMPBSA.py (for instance, try computing an RMSD). It would appear that
for some reason, cpptraj is hanging (which makes MMPBSA.py hang), and
without being able to investigate the files directly it's impossible to
know what's going wrong.
Good luck,
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
Received on Tue Sep 08 2015 - 07:30:05 PDT
