On Thu, Dec 28, 2006, Piotr Cieplak wrote:
>
>
> Apparently my calcium ions "C0" that have atom numbers: 2459, 2460, 2461
> are treated as "C" atoms in mdread.f of sander around line: 1200.
The surface-area facility in sander is based on the LCPO algorithm (see
references in the Users' Manual) and this only has parameters for the common
organic atoms and functional groups. Someone should step up to the plate
and program in a more general surface-area facility. Of course, it's not
clear that any surface-area model will make much sense for calcium ions
anyway....
For now, turn on gbsa.
...regards...dac
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Received on Sun Dec 31 2006 - 06:07:35 PST
