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:
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:
Then you also have NAMD and GROMACS, which are more robust when it
comes to energy minimization.
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/
> Does anyone happen to know of any other programmes accepting PDB
> structures for energy minimisation?
> 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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