Re: solvating long protein

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Oct 03 2007 - 14:04:25 CDT

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Hi,

On Wed, Oct 03, 2007 at 01:54:47PM -0500, Dhiraj Srivastava wrote:
> Hi All
> distance between two ends of my protein is around 150 A and is
> horseshoe shaped. I am using the command "solvate prodh.psf prodh.pdb -t 10
> -o prodh_wb". is it correct or do i need to take any precaution like need to
> reorient my system so that its length allign with any particular direction
> etc?

You probably want to use the option -rotate to minimize the volume of
the water box.

Cheers,
Leo

PS: This kind of question should probably be directed to the vmd-l
mailing list instead.

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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