On Fri, May 09, 2014, Guqin Shi wrote:
>
> I was using the XMIN method in NAB package to minimize my
> complex(protein+small molecule). The reason I am doing that is I want to
> further calculate entropy by using nmode() in NAB.
>
> I was trying to use PB solvent in minimization and below is my input:
This won't work, for at least two reasons:
1. The only implicit solvent model that has second derivatives (needed
for nmode()) is igb=1.
2. The xmin minimizer has strong assumptions about the accuracy of the forces;
numerical procdures like PB or RISM don't satisfy these conditions. So you
would not likely be able to do a full minimization anyway.
Finally, your particular allocation error suggests that you are asking for
more memory than you have available. You don't give enough details about
"changing the spacing parameters" to be very helpful (at least to me).
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 09 2014 - 13:00:02 PDT
