AMBER Archive (2009)

Subject: [AMBER] ptraj utility

From: Neha Bharat Gajaria (n.gandhiau_at_gmail.com)
Date: Tue Dec 01 2009 - 02:30:07 CST

Hi List,

I m trying to extract the distance between two Calpha atoms from amber
trajectories using ptraj. The average distance should be 10.05 Ang. After
50ns or so, the distances reported in the output are very unusual.

The output looks like
9.45
9.85
.
.
.
40.23
33.12

.
.
.
8.10
8.93

Are some of the trajectories corrupted or something is going wrong with the
box? thanking you for your response 

-- 
Regards,
Neha Gandhi Gajaria,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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