Re: [AMBER] question about bond command

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 22 Jul 2010 10:43:58 -0700

> I have a quite large organic molecule (2000 atoms) that I
> represented in terms of 4 different residues (rea, reb, rec, red).
> These residues lib and frcmod were built using antechamber.
> Of course the molecule is composed of these residues (30 rea,
> 40 reb, 50 rec, and 30 red) that are bonded in a certain way.
> I want to know whether I should use bond command to bond the
> residues to each other?

Yes. You can get sequential residues in pdb to auto-bond on
leap loadpdb if the templates have head/connect0 and tail/connect1
atoms defined, but this will only give you a linear chain topology -
for anything else you have to use the bond cmd.


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Received on Thu Jul 22 2010 - 11:00:04 PDT
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