ADL: Energy Minimization

L. Michel Espinoza-Fonseca mef at ddt.biochem.umn.edu
Thu Mar 6 11:20:59 PST 2008


Yes. For small molecules you can use VEGA:

http://www.ddl.unimi.it/vega/index.htm

This is a free program that can perform energy minimization at
semiempirical level. Pretty good and easy to use.

For proteins, the easiest program to use is the Swiss PDB viewer:

www.expasy.ch/spdbv/

Then you also have NAMD and GROMACS, which are more robust when it
comes to energy minimization.

Cheers,
Michel

On Thu, Mar 6, 2008 at 1:07 PM, George Tzotzos <gtzotzos at mac.com> wrote:
> The Dundee PRODRG2 Server has the functionality of energy
>  minimisation (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
>  prodrg.html)
>
>  Does anyone happen to know of any other programmes accepting PDB
>  structures for energy minimisation?
>
>  Thanks
>
>  George
>
>
>  On Mar 6, 2008, at 6:11 PM, Mihaly Mezei wrote:
>
>  >
>  >
>  >> Is energy minimization necessary since autodock is just going to
>  >> twist the molecule around anyway?  It seems like an unnecessary
>  >> step to me, and it looks like that is what you just quoted in from
>  >> the J. Comp. Chem. article.
>  > Actually, it is important to energy minimize, since the binding
>  > free energy estimate includes the energy of the ligand in the
>  > initial conformation. I once found a ligand whose binding free
>  > energy was estimated as ca -50 kcal/mol, due to some clashes int he
>  > initial conformation.
>  >
>  > Mihaly Mezei
>  >
>  > Department of Structural and Chemical Biology, Mount Sinai School
>  > of Medicine, NYU
>  > Voice:  (212) 659-5475   Fax: (212) 849-2456
>  > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/
>  > profile.do?id=0000072500001497192632
>  > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
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