Re: [AMBER] question about bond command

From: Philippe Pinard <>
Date: Thu, 22 Jul 2010 19:38:33 -0700 (PDT)

Thanks a lot, I will definitely do this to be sure about my commands.
How about one of my residues that has 4 bonds, Is it a must to use connecX, or
bond command should give the right results?
I looked to the amber tutorials, and couldnt find anything about how to define
connect2 and connect3 atoms, before creating the residu corresponding lib file.


From: case <>
To: AMBER Mailing List <>
Sent: Fri, July 23, 2010 2:58:12 AM
Subject: Re: [AMBER] question about bond command

On Thu, Jul 22, 2010, Philippe Pinard wrote:
> I am still confused whether or not I should use the bond command to bond the
> residues i defined with antechamber inside my pdb molecule.

For "standard" residues (in the Amber library), you don't generally need bond
commands, except for things like disulfide bonds.

When you define your own residues, it should work the same, but it's worth
double-checking. The "desc" command (on the entire unit, not just individual
residues) can help. Somehwhat easier is to run rdparm on the prmtop file you
create, and print out all bonds. If you are confused, you should definitely
do this -- it's a simple way to check that you are getting what you want.


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Received on Thu Jul 22 2010 - 20:00:04 PDT
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