I am trying to do a SBMD simulation on Nucleoside-Protein system.
The nucleoside (Inosine or Ade) in all the crystal structures (with substrate and substrate analogues) have phase angle(P) of 233-236 deg (C4' endo). When I start MD on this structure, within 300ps, the P changes to C3'-endo or C4'-exo (predominantly C3'-endo).
My questions - 1) Is it common to observe such changes in P during dynamics?
2) Does CHARMM (par_all27_prot_na.inp parameter file) biases the system towards one favored P (say C3' endo or C2' endo)?
3) Is it possible to parametrize par_all27_prot_na.inp parameter file to give the structure with desired P(=233)? It would be of immense help to me if you can point out the dihedrals that I should modify to favor my desired conformation.
4) Lastly, Is it possible to differentiate whether this conformational change is not an calculation artifact, but something that enzyme active site does. The last question is something that I would like to explore for my own satisfaction and validity of the results from MD.
I would appreciate the comments.
Thank you for your time.
Last edited by alex; 03/11/04 11:04 PM.