From: Ben Chern (
Date: Thu Mar 27 2008 - 06:35:56 CDT

As I don't major in Chemistry and Biology, I don't know the answer before.
But now, I know what the difficulty is.
If I want to visualize the interactions responsible for the primary
and secondary structure, would you give me some advice or suggestion? Is
there any reviews whick can help me understand the problem?
Thank you very much.

On Thu, Mar 27, 2008 at 12:19 PM, Axel Kohlmeyer <> wrote:

> On Thu, 27 Mar 2008, Ben Chern wrote:
> BC> Hello,
> BC> as we know, the interactions between different part is the reason of
> the
> BC> protein conformation.
> BC> Then can VMD detect and show the interactions that is reponsible for
> the
> BC> protein conformation in every scale(primary, secondary, tertiary and
> BC> quarternary structure)?
> of course not. VMD is a _visualization_ program. it only shows
> information that you feed it. the interactions itself have to
> be modeled with some method (forcefield, quantum chemistry etc.).
> those are a complex interplay of multiple types of interactions
> (short range and long range) and "volume" and/or entropy. if you
> could disentangle it that easily there would be no reason for
> projects like folding_at_home and so on...
> cheers,
> axel.
> --
> =======================================================================
> Axel Kohlmeyer
> 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.