AMBER Archive (2006)

Subject: Re: AMBER: Curves and Average Structures

From: David E. Konerding (dekonerding_at_lbl.gov)
Date: Mon Jun 26 2006 - 14:42:05 CDT

Lauren O'Neil wrote:
> Dear All,
>
> I have been using Amber to do MD simulations of DNA containing thymine
> dimer(s). I know that this listserv is not for Curves, but I figure a
> fair number of people must use it. I use Curves in the analysis of my
> simulations and have noticed that it will only accept a snapshot, not
> an average structure. I read a previous post that also said that this
> was the case. Does anyone know why? I have used curves on snapshots
> from my simulations from a time point where the RMSd seems "stable".
> Does anyone have any other suggestions for picking time points? Would
> it be possible to run multiple Curves analyses in some sort of
> automated fashion (I'm sure anyone who has used it knows that there is
> significant modification that has to be done to the pdb file)...I have
> a script that modifies my .pdb files, but doing multiple (over 100 or
> so) structures would be time consuming. Any suggestions would be
> much appreciated.
Lauren,

My guess would be that when you average your structures, you have some
geometry which is far
from ideal; for example, averaging a 50-50% mixture of C2' endo and C3'
endo gives you a sugar pucker
which does not exist in nature and has a very high energy. Usually you
should be able to fix this by minimizing
the average structure for about 100 steps.

I found X3DNA to be a much more usable program than CURVES. Alas, it
also is not capable
of working on large numbers of structures at a time. Dials and Windows
could do that (straight from trajectory files, no less); here is an
updated site for D&W:

http://ludwig.chem.wesleyan.edu/~wwang/mdtool/

I can't imagine why converting PDB files would be time consuming. It's
a simple transform to massage into CURVES, and then running CURVES takes
almost no time at all.

Dave
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