Re: [AMBER] question about bond command

From: Philippe Pinard <>
Date: Thu, 22 Jul 2010 12:16:38 -0700 (PDT)

concerning connect command: my residu connects to others using 5 atoms.
I never used connect command, is this to define head and tail?

From: Bill Ross <ross.cgl.ucsf.EDU>
Sent: Thu, July 22, 2010 7:50:28 PM
Subject: Re: [AMBER] question about bond command

> do I have to do in tleap: bond pdbname.REA.N75 pdbname.REB.C2

Sounds right - won't cost you to try it.

Technically if your residue connects to others using more than 2
atoms, you should also set connect2, connect3 etc. as needed
when defining the residue. Not sure what happens if you bond
without doing this.


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