Hi,
> Does anybody know what is wrong with the output from a simple CARNAL
> averaging. The pdb file of the average structure can not be visualized
> with any software and I also can not use it afterwards for calculating
> the rmsd of each frame to the average structure. The script is below:
> FILES_IN
> PARM p1 ../rna_ion_wat.top;
> STREAM s1 ../00.crd.gz ../01.crd.gz ../02.crd.gz ../03.crd.gz
> ../04.crd.gz;
>
> FILES_OUT
> COORD crd AVG.pdb PDB;
> DECLARE
>
> OUTPUT
> COORD crd s1 AVERAGE;
>
> END
Before calculating the average structure, you should fit (RMS FIT ...)
your solute onto a common reference (e.g. the first snapshot of your
trajectory) to reduce distortions from drift or pressure scaling. You
also might consider averaging over the solute atoms only (e.g. "COORD
crd s1 AVERAGE ATOM n" where "n" is the number of the first atoms of
interest in each snapshot).
Best regards
Holger
--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037 USA
phone: +1-858-784-9788
fax: +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Mon Sep 02 2002 - 13:43:52 PDT
