AMBER Archive (2006)

Subject: AMBER: PTRAJ: radius of gyration

From: kepa koldo burusco (kepaquestions_at_yahoo.es)
Date: Fri Nov 10 2006 - 11:05:09 CST

[10-XI-2006]

Hi amber users,

I'm trying to do a ptraj analysis on a Molecular
Dynamics simulation. I have the trajectory file
(single molecule in vacuum, already stabilized) and I
would like to get some information about the 3D
structure. In particular, I'm now interested in the
"radius of gyration".

I've been looking up in the manual's ptraj-section for
any clue but I didn't find anything (by the way, we
mainly work with amber 7). I've also been having a
look at CARNAL and also ANAL sections but neither I
find anything.

I think it is possible to do such calculation with
amber (I heard it anywhere). Can you help me? Does
anyone have any ptraj-input file as an example?

Thank you very much.

Kepa K. Burusco
Universidad Autonoma de Barcelona
BARCELONA (Spain)

                
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