AMBER Archive (2005)

Subject: AMBER: ptraj distance mask

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Wed Nov 02 2005 - 11:04:48 CST


All:

I am trying to measure the distance between four aromatic rings of two
non-standard residues, each residue has two aromatic rings. I'd be
happy just to get the distance between the centers of each ring and the
'distance' command seems appropriate for this but I'm having difficulty
with the mask.

The residues are call FLP and DAP. The atoms that comprise the rings
of FLP are C1-C6 and C7-C12 (and there are three additional carbons).
In DAP, the numbers are not contiguous in one ring and run C1, C2, C9,
C10, C11, C12. The are contiguous in the other ring (C3-C8).

What :mask could I use to define each of these rings. Thanks.

Pete
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