ADL: Solvation Parameters

Garrett M. Morris garrett at scripps.edu
Thu Sep 9 19:11:57 PDT 2004


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
>
>
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Dr Garrett M. Morris, MA, DPhil

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