Dear Amber users:
We've been testing some parameters for non-coded amino acids!
One test we would want to perform is the comparison between the energy profile of the MM calculated profile and an QM calculated profile!
I know Amber does not support any option to do this automatically, but I was hopping we could restrict the dihedral to a fixed value, perform an optimization on the hole unit and then (after frreiing the restriction) perform a single point to have an MM energy read!
It would be necessary to do this to each point of the profile!
We've been trying to use restraintorsion unit a1 a2 a3 a4 999999999 danglevalue 1 in xleap to keep the dihedral on the disered value but we are not achiving this objective.
Unless we are wrongly difining the atoms (we use unit.residuenumber.atomname) we don't understand the obtained values! We would expect a constrain en value of zero for the first point of the optimization (because the starting geometry has the desired value), but we don't.
Even worst is the fact that the restrain decreesses it's value when moving away from the value difined by us!
We belive that the restrain is not being correctly aplyed by us.
Can anyone help us on this?
Sincerely yours
Marco Preto
Ph. D. student
FCUP - Porto
Portugal
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Received on Fri Aug 01 2003 - 12:53:01 PDT
