Hi Jason,
'noimage' works..
Thanks a lot!
> On Thu, Dec 19, 2013 at 7:47 AM, <agarai.physics.iisc.ernet.in> wrote:
>
>>
>> Hi all,
>>
>> I want to calculate the end-to-end distance of a DNA molecule using
>> ptraj.
>>
>> I used the following input file:
>>
>> trajin md_prod_38_ns.trj
>> trajin md_prod_39_ns.trj
>> trajin md_prod_40_ns.trj
>> trajin md_prod_41_ns.trj
>> trajin md_prod_42_ns.trj
>> trajin md_prod_43_ns.trj
>> trajin md_prod_44_ns.trj
>> trajin md_prod_45_ns.trj
>> trajin md_prod_46_ns.trj
>> trajin md_prod_47_ns.trj
>> trajin md_prod_48_ns.trj
>> trajin md_prod_49_ns.trj
>> trajin md_prod_50_ns.trj
>> distance dist_tail_nuc :1,76 :38,39 out distance_dna_end
>>
>
> Try adding the "noimage" keyword here. If your DNA chain is large
> compared
> to the size of the box, then the distance cpptraj is calculating might be
> the distance between the head of the nucleotide sequence to the tail of
> the
> nucleotide sequence in the adjacent box. By default, cpptraj always takes
> the minimum distance between two masks among all of the periodic images.
>
> The mask :1,76 corresponds to resid of the residues at one end of the DNA
>> and the mask :38,39 correspond to the residues on the other end. Using
>> This input file, ptraj must calculate the distance between the center of
>> mass of residues 1,76 and 38,39. But the values that I get as output are
>> very much smaller than the expected values. I have checked the
>> trajectory
>> files and the .prmtop file and they seem to be fine. I am in doubt,
>> whether my input file is wrong or is there some other source for the
>> error. Kindly help.
>>
>
> Distances are very easy to compute, and as such are not very error-prone.
> If the image issue is not causing the lower-than-expected distances, then
> you should visualize your trajectory in VMD (or some related program) to
> see if you can find anything wrong. This is _always_ a good idea (and
> with
> tools like VMD you can always check that the distances you measured in
> cpptraj are 'correct').
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Best regards,
Ashok
--
Research Associate
Department of Physics
Indian Institute of Science
Bangalore - 560012
India
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Received on Sun Dec 22 2013 - 01:00:02 PST
