I am trying to calculate distance between Center of mass of two groups of atoms located at two ends of my system using distance command in ptraj for AMBER trajectories. For calculating the distance between two atoms, its working well with the following input file,
trajin md_prod_45_ns.trj 1 1000 10
distance x_a :10@O3' :20@O3' out dist_list
But I am not able to mask the group of atoms correctly. Eg. if I want to measure the distance between the center of mass of O3' atoms of reside 10 13 15 to O3' atoms of 20 25 30, what syntax should I write in ptraj input file.
If someone has done this before could you please share your experience?
Hello,
the general syntax for those masks is
:@
where
can be a single number, a comma-separated list, a continous list marked with a "-", or a combination thereof; omitting requests ptraj to use all;
can be a single name or a comma-separated list.
Examples:
:1-10,12,14@C,CA,N
-> Backbone atoms of residues 1-14 without 11 and 13.
In your case, something like :10,13,15@O3' should work; note, that there must be no spaces within the comma-separated lists.
In any case, further details about the masks can be found in the Amber(Tools) manual; see especially the tool ambmask.
Regards,
Anselm
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