VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Oct 27 2011 - 09:54:06 CDT

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On Thu 27, Oct 10, 2011 16:09:53 hamze rahimi wrote:
> Dear expert
>
> I want find average pdb from pr.dcd file as final pdb for docking. I think
> following method be helpful:
> 1- load pr.dcd file by using bigdcd
> 2- convert dcd to pdb file
> 3- using mergepdb script
>
> Please let me know if there are other scripts or idea in this subject
> many thanks in advance
>
Don't use a average structure, thats a bad habit.
Calculate the centroid (average structure) and then search for a real
structure close to the centroid (minimal RMSD).

To answer your question:
Use Google and search the Mailinglist, this has been addressed a lot of times.
http://goo.gl/k2uHf

Kind regards,
Bjoern

- --
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale

Phone: +49-345-55-24942
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