Hi,
I am trying to do a global RDC refinement, but the molecule appears to
move very little, or not at all.
My script goes as follows (Temperature = 300K over entire script)
1. Read structure, parameters, restraints (NOE, RDCs, dihedrals)
2. Introduce alignment tensor (pseudoatoms)
3. fix helices:
constraint fix=((segid SANI and resid 500)
or (segid EDHB and resid 1:5) or (segid EDHB and resid 33:37) or
(segid EDHB and resid 14:29)) end
My structure contains 37 residues, RDCs need to be refined for the
residues which are not fixed.
4. 4000 verlet dynamic steps of 0.0005 ps with the
flags bonds angle impr vdw noe cdih plan sani
5. Loop of verlet dynamics in which in every loop step the NOE and cdih
force is increased
6. 20000 verlet dynamic steps of 0.0005 ps, at 'high' force for NOE
and cdih
7. powell minimisation of 10000 steps
Any ideas are welcome.
Increasing the timesteps moves the final structures to a higher energy
level (and thus not ending up in an energetic minimum).
Is another temperature needed ?
Kind regards,
Ramon
