Hi Case,
Thanks for the suggestions. However, I cannot figure out why the CN length
is 0.2 for the 2nd CN- ion. I am still working at it. I also changed the
names to EP1 EP2, EPC EPN, LP1 LP2, nothing worked :( :(
I had another question::
Is it possible to constrain a bond of a tagged molecule? I mean, if I want
to tag the 2nd CN ion and contrain the bond (since I guess there is a
misflow of information on the coordinates of N being replaced by EP1 ) ?
~Surma
On Fri, 9 Sep 2011 17:43:43 -0400, case <case.biomaps.rutgers.edu> wrote:
> 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 Sat Sep 10 2011 - 12:00:02 PDT
