On Thu, Aug 04, 2011, Bin Wu wrote:
>
>
> I have a question about charge assigning method. It is my understanding that
> AmberTools has provided several partial charge assigning method including
> resp, gasteiger, bcc and etc. I wonder which charge method is mostly
> compatible with GAFF force field. BTW, I intend to simulate dendrimer
> (Poly(amido
> amine)) under neutral and protonated conditions (i.e. with NH3+ groups
> present.).
You should use gaff and antechamber to parameterize small pieces (monomers)
of your dendrimer, *not* to get charges for an entire polymer.
>
> I tried to use bcc once (under antechamber). It works very well at low
> generations, which has about 282 electrons. However, as the generation goes
> higher, e.g. at generation 1 which possesses about 778 electrons, the
> antechamber kept running and did not seem to stop after 14 hours.
The bcc charge procedure is trying to fully optimize (to a pretty strict
criterion) your input molecule. This was designed for small monomers with few
floppy degress of freedom. Admittedly, sqm "ought" to be able to geometry
optimize a system with 778 electrons (or give better diagnostic and error
messages), but this is well outside its design parameters.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 05 2011 - 07:00:02 PDT
