Thank you Jason for the input. I will try and get back if any issues occur
On Fri, Feb 13, 2015 at 6:04 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Feb 13, 2015 at 2:48 AM, Ayesha Fatima <ayeshafatima.69.gmail.com>
> wrote:
>
> > Dear All,
> > I have run 25ns of simulation using amber 12 and am interested in doing
> > hbond analysis of the binding site residues only. I searched round on the
> > mailing list and various tutorials and found some files which i modified
> > accordingly and used. The input file using residue names ran very well
> but
> > the input with residue numbers as given in Amber tutorial B3 is giving me
> > problems. it crashes without any reason at a specific step when it starts
> > to process the trajectories.I am attaching both the input and output
> files.
> >
>
> This is something I found in your output file:
>
> Estimated memory usage for this hbond call: 815.12 GB
>
> Unless you're using some kind of Altix machine, there's no way your
> machine has that much RAM, so what's happening most likely is ptraj ran out
> of memory. (As an aside, reading through the output file can often uncover
> enlightening nuggets like this that will suggest an appropriate solution).
>
> You will have to adjust your donor and acceptor masks. In particular:
>
> PTRAJ: donor mask .O
> Mask [.O] represents 32742 atoms
>
> This mask selects over 32K atoms, each of which pairs with a donor. You
> need to keep the pairs of donor and acceptor masks reasonable for ptraj to
> handle.
>
> As an alternative, I highly suggest switching to cpptraj in AmberTools 14
> and using the hbond command there. It is quite a bit easier to use (no
> need to set up lots of donor and acceptor atom masks). See pages 530 to
> 532 of the Amber 14 manual for a detailed description of the hbond action,
> and feel free to experiment with some of the options to get an
> understanding of how it works.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Feb 13 2015 - 07:00:02 PST
