CHARMM Development Project
Posted By: dna sugar pucker in c27 NA parameters - 02/13/04 07:08 PM
HI All,
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.

Posted By: alex Re: CHARMM v27 parameters for Nucleic Acids - 02/14/04 05:14 PM

Sugars are quite flexible and their puckers sample a wide range
during MD simulations. For that and your remaining questions
it would seem that you need to read some of the literature on
MD simulations of nucleic acids to get a better understanding
of the behavior of DNA. There are also examples of DNA-protein
calculations (we have some, as does Lennart Nilsson). One
place to start is with the CHARMM27 parameter papers; the
supplemental material (which is actually the entire paper)
can be obtained from my web page.

Also, don't necessarily take a crystal structure as "truth." Depending on resolution etc.
they may not be able to properly assign the pucker.

Posted By: hlwood Re: CHARMM v27 parameters for Nucleic Acids - 02/17/04 10:50 AM
This thread has been moved to Parameter Set Discussion
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