Re: [AMBER] how to simulate a polyester?

From: FyD <>
Date: Wed, 17 Sep 2014 12:12:35 +0200


If you use PyRED at R.E.D. Server Dev. the format generated by default
for FF libraries is the mol3 file format; see:

in this format, the head/tail are automatically generated;

see the keyword MOLECULE1-MOL3HEAD = ON if you need to modify the default.

regards, Francois

>> 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.

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Received on Wed Sep 17 2014 - 03:30:02 PDT
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