AMBER Archive (2009)

Subject: [AMBER] ACE and NME patch: VMD ???

From: Siddharth Rastogi (
Date: Mon Aug 31 2009 - 19:25:47 CDT

Dear AMBER Users,

I am using the AMBER prmtop and crd files in VMD to generate the box
information, which can be useful in running the MD in the NAMD suite.

However my prmtop file contains the information of ACE and NME patches,
which is compatible with the VMD or not I dont know ?After loading the
files VMD complains "Unusual bonding between the patch and the nearby

Can anyone suggest how to overcome the problem and the AMBER prmtop and crd
can be used to run the MD in NAMD ?

Your suggestions will be higly appreciated.

Siddharth Rastogi
AMBER mailing list