AMBER Archive (2008)

Subject: Re: AMBER: SPCFW problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Oct 28 2008 - 05:49:37 CDT

On Mon, Oct 27, 2008, Naser Alijabbari wrote:

> I am having problems getting the SPCFW water working.
> steps in tleap (I have added "?." To keep the file short):
>
>
> Error: A residue defined as a "fast 3-point water"
> is not defined by a triangle of three bonds.

Try setting jfastw=4. Of course, this should not be necessary, since you
didn't ask for SHAKE anyway. But the code calls a setup routine for SHAKE,
even when SHAKE has not been invoked :-(

And, check the calculations carefully. As you can tell, not many Amber
calculations have actually been done with flexible waters. You may need quite
a short time step to get good results.

...dac

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