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#8628 - 10/25/05 03:40 AM Centering a protein inside a water box
zee Offline
Forum Member

Registered: 07/05/04
Posts: 53
Hello.
I have protein that I've put inside a
water box of known size. I would like to center the protein inside the water box.
Many molecules of water are overlapping with the protein but I will remove them afterwards.

thanks in advance,
zee

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#8629 - 10/25/05 02:15 PM Re: Centering a protein inside a water box [Re: zee]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8389
Loc: 39 03 48 N, 77 06 54 W
It's best to orient the protein before combining with the water box. Assume the protein is SEGID A, then

coor orient sele segid A end

will both center and rotate the protein, to align the longest dimension of the protein along the Cartesian X axis. To suppress the rotation, use

coor orient sele segid A end norot

See corman.doc for details on COOR ORIENT and other commands that manipulate or analyze coordinates.
_________________________
Rick Venable
computational chemist


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#8630 - 10/27/05 02:52 AM Re: Centering a protein inside a water box [Re: rmv]
zee Offline
Forum Member

Registered: 07/05/04
Posts: 53
thank you!

zee

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