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
>>
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Received on Thu Jul 23 2015 - 01:30:02 PDT
