Re: [AMBER] Solvate box

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 26 Jan 2011 11:44:42 -0800

> solvatebox x TIP3PBOX {5 5 5}

Note this should be equivalent to

solvatebox x TIP3PBOX 5

> It constructs the solvated sample .Is there way of controlling how many
> molecules of solvent molecule I want to add.

Only crudely, by changing the clearance or the (commonly unused)
closeness parameter. Note that you have to make a new copy of
x before each try. You could also delete solvent molecules once
added, e.g. graphically in xleap or probably in tleap tho I forget
the command. Another approach would be to savepdb, delete in the
pdb, then loadpdb and setbox.


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Received on Wed Jan 26 2011 - 12:00:02 PST
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