RE: AMBER: Is there a way to simulate a box of pure water with amber

From: Ross Walker <>
Date: Fri, 15 Dec 2006 10:52:53 -0800

Dear Li,

> Sorry to bother. I am wondering if there is a way in amber
> to construct a
> box of water with no protein for simulation. Thank you in advance.

Assuming you have all the latest bugfixes installed the following should work in xleap.

edit tempunit

'will create tempunit and bring up an empty window. Close it.'

solvatebox tempunit TIP3PBOX 10.0

Will give you a 20A across box of tip3p water.

saveamberparm tempunit waterbox.prmtop waterbox.inpcrd

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Dec 17 2006 - 06:07:20 PST
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