OK, based on your input I think I know what is happening here. You are
using an averaged structure as a reference, so that structure is changing
based on how many frames go into the average (which is why you see
different contact pairs reported when you increase the # of frames).
Using an averaged structure as a reference is a bad idea in my opinion.
They tend to be very unrealistic, particularly when there is significant
internal motion (e.g. a rotating PHE ring will "flatten out" and become
almost a straight line). You should use a real structure as your reference
for 'nativecontacts', otherwise the contacts you come up with will likely
not represent actual contacts. If your system has a crystal structure
available that may be a good candidate, or perhaps a properly equilibrated
structure.
Hope this helps,
-Dan
On Thu, Jul 23, 2015 at 1:59 AM, Juan Eiros Zamora <
j.eiros-zamora14.imperial.ac.uk> wrote:
> Hi,
>
> I'm attaching the failed output files. The cpptraj (my version is V15.00)
> commands I'm using are:
>
>> parm top.prmtop
>> trajin phos_all.nc
>> rms first
>> average crdset average_structure
>> createcrd loaded_trajs
>> run
>> crdaction loaded_trajs rms ref average_structure
>> nativecontacts :1-89 :396-412 ref average_structure byresidue resout
>> cmap_1.dat
>> nativecontacts :1-89 :386-395 ref average_structure byresidue resout
>> cmap_2.dat
>> nativecontacts :1-89 :249-289 ref average_structure byresidue resout
>> cmap_3.dat
>> nativecontacts :249-289 :386-395 ref average_structure byresidue resout
>> cmap_4.dat
>> run
>>
> I've tried using an offset of 1000 when calling the trajin command, but
> still getting the same errors. But on shorter trajectories the output files
> are printed fine.
>
> All the best,
>
> Juan
>
>
>
> On 22/07/15 21:53, Daniel Roe wrote:
>
>> Hi,
>>
>> What version of cpptraj are tou using? Also, can you provide your cpptraj
>> input and output? Thanks,
>>
>> -Dan
>>
>> On Wednesday, July 22, 2015, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> Hi everyone,
>>>
>>> I've got a large trajectory file obtained from different independent
>>> runs and I want to use the nativecontacts command to analyze it.
>>>
>>> I have 4 nativecontacts analysis to do, which work fine if I use a
>>> subset of the data. But if I load the whole thing, the contact residue
>>> pairs files come up incomplete (some have only a subset of the pairs,
>>> and the last one only has the header). All those files are written
>>> properly if I use a small set of the data, so I'm guessing it's not a
>>> problem of the analysis per se.
>>>
>>> How can I figure out the offset I have to use when loading the big
>>> trajectory to minimise accuracy loss on the analysis? That's the only
>>> alternative that comes to mind, but I would like to use all the frames
>>> (even if it takes awhile) if that's possible.
>>>
>>> Thanks in advance for any suggestion,
>>> Juan
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 23 2015 - 09:00:04 PDT
