Re: script for calculation of an rmsd

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat Oct 30 2010 - 07:09:44 CDT

Maria,

You have built-in RMSD calculation tool in VMD, under analysis. Only
select atoms that you want for your molecule (antibiotic). Also you
should browse VMD user guide, particularly
http://www.ks.uiuc.edu/Research/vmd/current/ug/node194.html.

The second option is to use VegaZZ - also free as well as VMD and NAMD
are
(http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ)
there you find comfortable user interface for (really) widespread types
of trajectory analysis.

Regards

Branko

On 10/30/2010 10:41 AM, matziast_at_med.uth.gr wrote:
> Hi, I want to calculate the rmsd of an antibiotic with a script, but I have
> script only for proteins. Could anyone tell me where I can find. Also, I want
> to learn how to write script. I must read tutorials of tcl only or something
> especially for namd?
> Thank you in advance.
> Maria
>
>
>
>
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