Previous Thread
Next Thread
Print Thread
sugar pucker in c27 NA parameters
#935 02/13/04 07:08 PM
Joined: Feb 2004
Posts: 1
dna Offline OP
Forum Member
OP Offline
Forum Member
Joined: Feb 2004
Posts: 1
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.

Devleena

Last edited by alex; 03/11/04 11:04 PM.
Re: CHARMM v27 parameters for Nucleic Acids
dna #936 02/14/04 05:14 PM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782
Devleena,

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.

http://www.pharmacy.umaryland.edu/faculty/amackere/param/force_field_dev.htm

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

Alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: CHARMM v27 parameters for Nucleic Acids
alex #937 02/17/04 10:50 AM
Joined: Sep 2003
Posts: 119
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 119
This thread has been moved to Parameter Set Discussion


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.008s Queries: 20 (0.005s) Memory: 0.9039 MB (Peak: 0.9771 MB) Data Comp: Off Server Time: 2020-09-29 01:44:12 UTC
Valid HTML 5 and Valid CSS