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 hybridization… Is there any way to set the number of bonds between atoms explicitly?
Can anyone advice me on that?
Thanks,
Maxim
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 03 2014 - 12:00:02 PST
