On Fri, Sep 09, 2011, tsurma.umich.edu wrote:
>
> Now, I have added 2 CN- ions with extra points and 2 K+ ions, and SHAKE is
> failing at the 2nd CN-. I also noticed that the usiz (bond length) of the
> second CN- ions is read as 0.200 instead of 1.17 (0.200 is the C-EP
> length).
Can you track down why the ideal bond length of the second CN is 0.2? That
will clearly cause a SHAKE error.
>
> My question is ::: is it possible that since I added an extra frame type
> for CN-, SHAKE works fine for the 1st CN- and breaks for the second one?
> The way the molecules are lined up in prmtop file is
>
> C1 N1 P1 P2 C1 N1 P1 P2
There are parts of the extra point code that require extra point atom names
to begin with "EP". You might see if changing the names would make a
difference (wild guess).
...dac
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Received on Fri Sep 09 2011 - 15:00:02 PDT
