Hi,
Thanks for the suggestions.
I fixed the problem by changing the prepc file:
The system is C-N with C with two extra points : EP-C-EP--N
Initially, the prepc file had C as M (main atom) and N, EP, EP as E (end
points).
Now, I changed C (M) and N as M (main atom) and two EP as E (end atoms).
And now it works perfectly!!! (the ntf=ntc=3 works fine and the system
behaves normally).
I am not sure what is going on here, and the forces look a little funny as
well. Could you help me understanding the problem?
~Surma Talapatra
On Sat, 10 Sep 2011 20:17:26 -0400, case wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 14 2011 - 08:30:05 PDT
