ADL: Solvation Parameters

Garrett M. Morris garrett at scripps.edu
Sat Sep 11 21:38:52 PDT 2004


Dear Swayam,

On Sep 10, 2004, at 10:47 pm, swayam panda wrote:

> 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

This is a very good question.

You can be pretty certain if you obtain just one cluster at the end of 
the docking; 10 dockings per compound may be enough, but you are doing 
very "deep" dockings, at 50 million evals.  You might like to try 100 
dockings at 5 million evals, to compare the how best to "spend" the 
same number of energy evaluations ("evals").  See if you get reasonable 
docked conformations at the end of each kind of docking; 100 dockings 
is more likely to give you better clustering statistics.  If you start 
with random number generator seeds that are dependent on the time and 
process id (pid) of your docking (this is the deafult behaviour for 
AutoDock scripts like mkdpf3 and ADT), then you should get different 
results each time: remember that AutoDock's search methods, SA, GA and 
LGA, are all stochastic search methods, which means the outcome will 
vary depending on the random numbers generated during the docking.

You can be confident of convergence if you obtain the same 
conformations frequently or even always, and this will be reflected in 
the conformational clustering in the histogram at the end of the DLG 
(docking log file).  The clustering depends on the size of your ligand 
and the rmsd tolerance you use, but it is best to use an "rmstol" of  
about 2 Angsroms for your clustering.

I hope this helps,

Garrett

> 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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___
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




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