Hi Jianwen,
In Ross Walker's Workshop Tutorial #4, he is talking about editing the
structure (pdb) before putting it into xLeap.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
Is the type of water molecules (O atoms) defined as HOH? In the tutorial
it is defined as HOH.
Good luck.
On Mon, 20 Dec 2004, Jianwen Jiang wrote:
> Hi,
>
> I started with a pdb file with crystalline water molecules (O atoms
> only).
>
> With the water molecules removed, leap could run successfully to build
> top & crd files. However, without removing the crytalline water
> molecules, leap failed. Could some let me know how I can achieve this?
>
> Will the command "gwh" or "protonate" help?
>
> -
> Kind regards,
>
> Jianwen
>
> -------------------------------------
> Jianwen Jiang
> Department of Chemical Engineering
> University of Delaware
> Newark, DE 19716
> -------------------------------------
> Tel: (302) 831-6953
> Fax: (302) 831-1048
>
>
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>
--
Ilyas Yildirim
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Received on Tue Dec 21 2004 - 00:53:00 PST
