AMBER Archive (2006)

Subject: Re: AMBER: Curves and Average Structures

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Tue Jun 27 2006 - 03:57:47 CDT

I don't think that Curves has problem in analysing average structures,
the only issue is to make Curves recognizes your pdb file. Once you have
done this , it is possible to write a shell script which is capable to
run Curves in sequence in order to analyse a series of pdb files from
your simulation.
You can use ptraj to produce the pdb files, for instance:

trajin filename 2001 3000 2
trajout dna pdb
go

if you want 500 pdb files between 2ns and 3ns of your simulation.

Hope it helps

Angelo

David E. Konerding wrote:

> 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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