AMBER Archive (2001)

Subject: Re: Problems with AMBER

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jun 29 2001 - 18:23:06 CDT

        a question regarding carnal. I can specify residues but how do
        you specify exact atoms when using the distance calculation DIST. (For
        example, instructing the script to measure the distance between the
        N-terminal Nitrogen atom and the C-terminal carboxyl carbon).
        
You can't specify classes of pairs, (for all pairs between
two groups can be done with DISTRIBUTION DIST I think), but
simple pair-of-atoms distances, specify <atom_name residue_number>,
so

  DIST d1 N 1 C 2;

for N in res 1 to C in res 2.

Bill Ross