AMBER Archive (2004)

Subject: Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Dec 20 2004 - 18:42:29 CST


 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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