AMBER Archive (2006)

Subject: AMBER: question on distance calculation

From: bala (cbala_at_igib.res.in)
Date: Mon May 08 2006 - 05:09:23 CDT

Dear amber users,
 
I have done a 10ns simulation on a oligonucleotide with counterions and solvent. There are 22 counterions in the system. I want to know at each conformation in the trajectory, what are the ions, staying within say 5A from DNA or particular residue.
 
In the manual, no option is given for fixing min and max distance in the distance command in ptraj or the DIST command in carnal. can someone please write whether it is possible to track the ion distances in conformation wise with a distance criteria. For instance, the HBOND analysis in carnal is giving, what are the water molecules interacting with say atoms in a DNA residue at each conformation in the traj. I want to know whether similar calculation is possible with distance command for ions.
 
awaiting your suggestion,
Bala
 
 

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