Dear Amber users
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.).
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. At even
higher generations, I directly get an error of "Segmentation fault" when I
tried to invoke antechamber.
Another question would be will these charge method make qualitative changes
on the simulation results ? For instance, will the characteristic quantities
like radius of gyration depend sensitively on the charge assignment method
while I am using the GAFF force field?
Any comments and suggestion would be highly appreciated!
Thank you very much.
Bin
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Received on Thu Aug 04 2011 - 12:00:02 PDT
