Re: [AMBER] how to simulate a polyester?

From: Jason Swails <>
Date: Tue, 16 Sep 2014 11:18:58 -0400

On Tue, 2014-09-16 at 22:52 +0800, 张冬冬 wrote:
> Dear all,
> I want to ask a question that whether we could use amber to simulate a
> polyester. Recently, I have tried to construct a polyester which is
> produced undergoing condensation reaction by some same units
> containing a carboxyl and a hydroxyl. I tried to use the sequence
> command, it turned out, however, to be unsuccessful. The sequence
> command seems to work on amino aicd residues and does not recognize
> the unit containing carboxyl and hydroxyl, which means it can't bond
> these units to form the polyester. So I want to ask that whether you
> could give me some useful suggestions about this.

Actually the "sequence" command in tleap only works for residues that
have been defined and loaded and that have a defined HEAD and TAIL (or
connect0 and connect1) atom. By default, all of the standard force
fields load amino and nucleic acid residues. So those will always
appear to work.

If you want your polyester to be built by tleap, you need to create a
library file (mol2 or OFF) for each fragment, and then define a head and
tail atom for each residue.

You can see how this is done for the amino acid residues by looking at
the $AMBERHOME/dat/leap/parm/ff12SB.cmd file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 16 2014 - 08:30:02 PDT
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