Hello,
On Thu, Feb 4, 2010 at 5:50 AM, Francesco Pietra <chiendarret.gmail.com> wrote:
> Thanks. Now I am tempted to use "CZ" type for C of carbon monoxide,
> however I don't see any correspondence in parm99.dat for O of carbon
> monoxide. I would need triply bonded oxygen. Otherwise I could
> consider C=O, as it is written, for carbon monoxide, but it would be a
> bad choice and, if so, which carbon type?
Using O would probably not be a bad choice. The only thing you would
gain by using a new atom type would be the ability to choose new vdW
parameters for that oxygen. A CZ-O bond is not defined in parm99.dat,
so you can choose new equilibrium bond lengths and force constants
(even if it WAS defined, you could override that with an frcmod file,
but the fact that it's not there means you likely won't be
inadvertently changing other parameters). However, it may be good
practice to create new atom types for different molecules in this case
to make sure you avoid specifically this potential problem. You can
then probably copy vdW parameters from closely related atoms in the
parm file.
>
> As I am going to use a modified Amber8, I am limited by the
> availability in leaprc.ff99, but in AMBER10 leaprc.ff99SB I see the
> same situation.
This is not necessarily true. FF99 has many known problems, and using
it is ill-advised for publication-quality work. AmberTools 1.3 is
freely available, so you can download that and build a prmtop file
with ff99SB or ff03. As far as I know, any prmtop created with
AmberTools 1.3 is compatible with amber8.
> Before embarking in using inappropriate data, a suggestion would be
> greatly appreciated.
>
> francesco
Good luck!
Jason
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 04 2010 - 08:00:02 PST
