AMBER Archive (2009)

Subject: Re: [AMBER] parameters for O2 molecule

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Oct 22 2009 - 09:19:51 CDT


You can probably use the L-J parameters from the carbonyl O. The bond
length and vibrational frequency (which will directly give you the bond
force constant) should not be hard to find online or in the CRC (and should
be pretty easy to calculate with an ab-initio package anyway). Also, since
O2 is neutral and a dipole moment is symmetrically forbidden, I'd say that
the partial charge on each atom in a non-polarizable force field is 0. You
can use parmchk to create an frcmod file, and that'll show you the
parameters you have to fill in (but be careful to give it a name not
recognized by the force field you're using or it'll give partial charges
based on the pre-defined atom type). The parameter data file is located at
$AMBERHOME/dat/leap/parm so you can get relevant parameters from your
favorite force field. Good luck!

All the best,
Jason

2009/10/22 Jeffrey <jeffry20072008_at_yahoo.cn>

> Dear AMBER users,
>
> We are going to monitor the transport of O2 molecule by MD simulation.
> But I am not sure whether AMBER FF provides parameters of the oxygen
> molecule? If not, where can I get the parameters?
>
> Many thanks.
>
> Jeffery
> ----
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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