Re: [AMBER] visualising frame of minimisation

From: Jason Swails <>
Date: Thu, 17 Jun 2010 09:39:17 -0400


On Mon, Jun 14, 2010 at 12:02 PM, Alan <> wrote:

> Hello there,
> As far as I see it is not possible to generate a sequence of frames
> (preferably PDB) of sander during minimisation, am I wrong? If so, how?

I think Ben Roberts was working on that, or something similar, but I don't
know if he finished and/or if it found its way into the release version of
amber11. (He will have to comment here) This is assuming, of course, that
you're referring to this functionality in sander. A couple of work-arounds
would be to write a nab program to do this (using xmin) or scripting sander
to run a bunch of small minimizations, renaming the restart files each
time. For the latter, you pay the penalty of starting up sander x number of

Hope this helps,

> Many thanks in advance,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >> <><<
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jun 17 2010 - 07:00:03 PDT
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