ADL: Solvation Parameters

swayam panda swayam_25 at yahoo.co.in
Fri Sep 10 08:47:03 PDT 2004


hi ,
   
           I am trying to dock 100 ligands to a
protein .my lagands have 18 to 26 no of tortion .i am
using 100  populatiaon size ,no of run 10 and no of
energy evaluation is 50000000 .i wan to know what is
the convergense criteria.i am using Lga .i am unable
to know what should be the appropriate enery
evaluation and run and how i will know that it has
reached that convergense 
thanking you
swayam prakash panda 
IICT,HYd
INDIA
--- "Garrett M. Morris" <garrett at scripps.edu> wrote:

> 
> Hi Paul,
> 
> My best advice is to put the values in by hand after
> you have written 
> the PDBQS file, but you will have to look at the
> original Stouten paper 
> (or similar atom types in your protein) and compare
> the atom types in 
> your "non-standard" residues, selecting the values
> that most closely 
> match.
> 
> You can use ADT as well as addsol to add the
> solvation parameters.
> 
> I hope this helps,
> 
> Garrett
> 
> On Sep 9, 2004, at 2:01 am, Paul J Shrimpton wrote:
> 
> > Hi,
> >
> > I want to include non-protein residues in my
> receptor, I realise they 
> > should be included with polar hydrogens only and
> appropiate united 
> > atom charges but my question is do I need to add
> solvation parameters 
> > for the atoms in my extra residues?? If so how is
> the best way to 
> > obtain the values I will need as addsol or the add
> solvation params in 
> > adt only recognise "standard" protein residues??
> >
> > Thanks in advance,
> >
> > Paul
> >
> >
> >
> > -- 
> > Paul Shrimpton
> >
> > Structural Bioinformatics Group
> > Biochemistry Building
> > Department of Biological Sciences
> > Imperial College
> > London SW7 2AY, U.K.
> >
> > Tel: +44 (0)20 7594 5762
> > e-mail: p.shrimpton at imperial.ac.uk
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- 
> > http://www.scripps.edu/pub/olson-web/doc/autodock/
> ---
> >
> ___
> Dr Garrett M. Morris, MA, DPhil
> 
> The Scripps Research Institute,       tel: (858)
> 784-2292
> Dept. Molecular Biology,  MB-5,       fax: (858)
> 784-2860
> 10550  North Torrey Pines Road,       email:
> garrett at scripps.edu
> La Jolla,  CA 92037-1000,  USA.      
> www.scripps.edu/pub/olson-web/gmm
> 
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/
> ---
> 



		
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