[AMBER] Regarding distance between residue masks (ptraj)

From: <agarai.physics.iisc.ernet.in>
Date: Thu, 19 Dec 2013 18:17:13 +0530

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

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.


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Received on Thu Dec 19 2013 - 05:30:02 PST
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