AMBER Archive (2007)

Subject: AMBER: problems visualizing mdcrd in VMD

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Wed Oct 31 2007 - 05:17:21 CST

Dear all,
when I try to visualize trajectory in VMD programs I got great results only when I impose in my sander input file ntb=0.
When I use ntb=2 and I load prmtop and mdcrd in VMD, I get a disaster and it's not possible to recognize any molecule in the animation, every bond is stretched to several amstrong.
How can I visualize trajectory when I impose ntb=2?
There are others useful visualization programs?

Thanks in advance for your help.

Mattia Mori
 

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Mattia Mori, PhD Student
CERM - Centro di Risonanze Magnetiche
via L. Sacconi 6,,
50019 Sesto Fiorentino, FI
fax (+39) 055 4573914
tel (+39) 055 4573912
www.cerm.unifi.it
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