AMBER Archive (2004)

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

From: Jianwen Jiang (
Date: Mon Dec 20 2004 - 18:18:52 CST


I started with a pdb file with crystalline water molecules (O atoms

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 Jiang
Department of Chemical Engineering
University of Delaware
Newark, DE 19716
Tel: (302) 831-6953
Fax: (302) 831-1048

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to