AMBER Archive (2003)

Subject: Re: ptraj and rdf help

From: tianxiao yang (yang.984_at_osu.edu)
Date: Wed May 21 2003 - 17:54:59 CDT

Dear Prof.Case,

I want to view Metal-O and Metal-H RDF.
I am sorry I did not make it clear in my previous email.
Thank you very much for your kind help in advance.

Tianxiao Yang

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My MD system is one metal ion solvated in water. I have a big problem
running ptraj to draw RDF between solute central metal and WAT. Could you
please kindly help me out? I greatly appreciate your kind help.

My ptraj script file is:
trajin md02.mdcrd
center
radial cm-o-md00 0.05 8.5 :WAT_at_O :1_at_CM closest density 0.033456
radial cm-h-md00 0.1 8.5 :WAT_at_H2 :1_at_CM closest density 0.033456
go