Thanks to all for your contribution in understanding the problem.
About the parameters for ATP, in the REDdb database for cofactors, F90/F91.
It seems that the server is down now, so I could not paste the link here.
Hope it helps.
Have a nice day
2015-10-08 8:28 GMT+02:00 Jonathan Sheehan <jonathan.sheehan.gmail.com>:
> The addAtomTypes command is working, and seems to be the best solution.
>
> Many thanks, all!
>
>
>
> On Wed, Oct 7, 2015 at 10:06 PM, David A Case <david.case.rutgers.edu>
> wrote:
> > On Wed, Oct 07, 2015, Jonathan Sheehan wrote:
> >>
> >> The .prep and .frcmod files both refer to the atomtype "O3". They
> >> don't specify its atomic number, and I don't see a way to add that,
> >> using the current .frcmod format.
> >
> > Atomic numbers need to be added by an "addAtomTypes" command to LEaP.
> > (This actually establishes the element name, but that is converted to
> atomic
> > number internally in the code.) This is generally done in leaprc files,
> but
> > it can also be entered in any LEaP input file:
> >
> > AddAtomTypes {
> > { "O3" "O" "sp2" }
> > }
> >
> > It is arguably a bug-let that you can't put such information into the
> > frcmod file itself, since that would collect all relevant information
> > about a new atom type (like O3) into a single file. But the code that
> > reads the frcmod file is pretty primitive, and I'm not sure how easy it
> > would be to allow it to recognize and process AddAtomType commands.
> >
> > For how, use the workaround above.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 08 2015 - 01:30:02 PDT
