AMBER Archive (2006)

Subject: AMBER: Calculating native contacts for mdcrd files

From: Anna Bowman (
Date: Thu Oct 26 2006 - 10:20:50 CDT

Can anyone suggest a way of calculating native contacts from amber
trajectory (mdcrd) files? Is it is possible in ptraj or do I need
additional scripts? So far I have only found scripts that calculate this
for an ensemble of pdb files. However, I currently have ~5000 snapshots
from sander and would prefer not to have to convert them to pdb format. I
am using amber8.
Many thanks in advance,
Anna Bowman
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