AMBER Archive (2009)

Subject: [AMBER] Problem with radial distribution function

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Fri Jun 26 2009 - 03:56:09 CDT

Dear amber users,
                   How to avoid intra-residue interaction during RDF
calculation using ptraj?. For e.g, say I have a box contains 200 water
molecules( atom names as follows,H1-O1-H2) and I would like to calculate the
radial distribution of O1 with H2.

radial O1_H2 0.05 20.0 :WAT_at_O1 :WAT_at_H2

 But I want to make sure that the ptraj won't count the O1-H2 interaction
within the same residue. Can anyone help me in figure out this problem.
Waiting for valuable reply

Thanks in advance
Aneesh
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber