[AMBER] atoms with non-standard hybridization

From: Ivanov, Maxim <maxim.ivanov.marquette.edu>
Date: Fri, 3 Jan 2014 19:30:25 +0000

Dear AMBER Users,

I need to run MD for a system containing PF6 anion. Since phosphorous with six bonds is not defined in the standard force field libraries, I either can use the atom type that belongs to other type of phosphorous or define a new atom type.

In the first case, even though I define 90 degrees angle for F-P-F bond with large force constant, during the simulation the configuration of the anion is changed significantly and is not octahedral any more. I assume this is related to the predefined hybridization of the original atom. However, I am not sure how to add a new atom type with such non-standard hybridizationů Is there any way to set the number of bonds between atoms explicitly?

Can anyone advice me on that?
 
Thanks,
Maxim
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Received on Fri Jan 03 2014 - 12:00:02 PST
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