On Sat, Sep 10, 2011, tsurma.umich.edu wrote:
>
> 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 :( :(
Did you examine the prmtop file by hand, or use ptraj to print out the values?
With only a handful of atoms in your system (it sounds like you could make a
test case with just 8 atoms that would fail), it should be pretty easy to
figure out if the problem is in the prmtop file or in sander. (In other
words, either the prmtop file indicates that the second CN has a bond length
of 0.2, or your modified sander is misreading the prmtop file. We need to
find out which is the case in order to get any closer to solving the problem.)
>
> 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 ) ?
I don't know of any notion of a "tagged" molecule in Amber.
...dac
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Received on Sat Sep 10 2011 - 17:30:02 PDT
