AMBER Archive (2005)

Subject: Re: AMBER: average structure-ptraj

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Apr 09 2005 - 10:02:02 CDT

I'm not sure of the problem but I can think of 2 things:

1) you might want to fit your structures to a reference so that
you don't average over something that rotates/translates

2) is your structure changing much? averaging only makes sense for
very similar structures. if it is changing (flexible), the average will
indeed have problems. in that case you probably want to
use clustering or another method to get at what you want.

xueping wrote:

>Dear all,
>
>I am having problem again to generate my average
>structure using ptraj, this is my script:
>
>trajin ../PfCo.md1.mdcrd
>trajin ../PfCo.md2.mdcrd
>trajin ../PfCo.md3.mdcrd
>trajin ../PfCo.md4.mdcrd
>trajin ../PfCo.md5.mdcrd
>average PfCo_average.pdb pdb nowrap
>
>i viewed my PfCo_average.pdb file in vmd, the
>structure
>is not correct, in the vmd console, it stated that
>unusual bonding within certain residue to certain
>residue...
>
>then i try to convert my last rst file to pdb file n
>view it, it is ok...meaning my simulation shouldn't
>have any problem rite?
>
>I try to generate average structure using single mdcrd
>file, it gives me the same error too... Please give me
>some suggestions.
>
>Thank you very much..
>
>Regards
>xueping
>
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