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
Received on Wed Oct 07 2015 - 23:30:03 PDT
