AMBER Archive (2004)

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

From: Jianwen Jiang (jiangj_at_che.udel.edu)
Date: Mon Dec 20 2004 - 18:18:52 CST

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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