Thanks a lot for your quick response.
Actually the system is not that big, I only have around 700 atoms in the
molecule.
The restrained residues are just dummy atoms. I also checked the forces on
non-restrained atoms,and different force constants on restrainted atoms
does not make any difference in the force of non-restrained atoms.
Problem is with the second derivative calculation.Is there a difference
between the implementation of ntr option in sander and icons option in
nmode?
thanks again,
sebnem
<quote who="David A. Case">
> On Tue, Mar 28, 2006, sebnem.mercury.chem.pitt.edu wrote:
>
>> group
>> 1
>> RES 35 279
>> END
>> END
>
> I don't see anything obviously wrong, but this is a very big system to
> be doing normal modes on. If you want to explore things in more detail,
> try printing out the Hessian elements for a very small test case, and
> work your way up in size.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Sebnem Essiz
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 02 2006 - 06:10:09 PDT
