VMD-L Mailing List

From: Ben Chern (futuredream.1_at_gmail.com)
Date: Thu Mar 27 2008 - 20:26:13 CDT

Thank you for your suggestion.

On Thu, Mar 27, 2008 at 7:43 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
wrote:

>
> On Thu, 27 Mar 2008, Ben Chern wrote:
>
> BC> As I don't major in Chemistry and Biology, I don't know the answer
>
> nobody is perfect. ;-)
>
> BC> before. But now, I know what the difficulty is.
>
> hmmmm....
>
> BC> If I want to visualize the interactions responsible for the primary
> BC> and secondary structure, would you give me some advice or suggestion?
> Is
>
> primary structure is in the broadest sense the bonding
> and thus a given input (unless you have a chemical reaction
> that breaks and forms bonds).
>
> if there was a clean answer to what determines the secondary
> structure, a lot of researchers would have to look for new
> projects. in principle, everything contributes and how this
> can be decomposed into individual contributions, depends a
> lot on the level of detail you put into the model describing
> those interactions.
>
> BC> there any reviews whick can help me understand the problem?
> BC> Thank you very much.
>
> i think you need to learn, how molecular simulations as a
> whole do work. for that a text book like
>
> A. R. Leach
> Molecular Modeling - Principles and Applications
> Prentice-Hall, 2001
>
> may be a good starting point.
>
> cheers,
> axel.
>
> BC>
> BC> On Thu, Mar 27, 2008 at 12:19 PM, Axel Kohlmeyer <
> BC> akohlmey_at_cmm.chem.upenn.edu> wrote:
> BC>
> BC> > On Thu, 27 Mar 2008, Ben Chern wrote:
> BC> >
> BC> > BC> Hello,
> BC> > BC> as we know, the interactions between different part is the
> reason of
> BC> > the
> BC> > BC> protein conformation.
> BC> > BC> Then can VMD detect and show the interactions that is reponsible
> for
> BC> > the
> BC> > BC> protein conformation in every scale(primary, secondary, tertiary
> and
> BC> > BC> quarternary structure)?
> BC> >
> BC> > of course not. VMD is a _visualization_ program. it only shows
> BC> > information that you feed it. the interactions itself have to
> BC> > be modeled with some method (forcefield, quantum chemistry etc.).
> BC> >
> BC> > those are a complex interplay of multiple types of interactions
> BC> > (short range and long range) and "volume" and/or entropy. if you
> BC> > could disentangle it that easily there would be no reason for
> BC> > projects like folding_at_home and so on...
> BC> >
> BC> > cheers,
> BC> > axel.
> BC> >
> BC> > --
> BC> >
> =======================================================================
> BC> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> BC> > Center for Molecular Modeling -- University of Pennsylvania
> BC> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> BC> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> BC> >
> =======================================================================
> BC> > If you make something idiot-proof, the universe creates a better
> idiot.
> BC> >
> BC>
> BC>
> BC>
> BC>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

-- 
Ben