Dear Jason,
You pointed out very correctly, it was only memory issues. i ran one
trajectory without offering any masks, it required only 8GB of memory. Now
I would like to ask another thing. Is it possible to get any information
about the ligand in the complex as does not belong to any standard amino
acid groups. How can we detect information about nonstandard residues using
the hbond facility?
thank you
On Fri, Feb 13, 2015 at 10:40 PM, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Feb 14 2015 - 04:30:02 PST
