Re: [rDock-list-def] Phosphoserine

[Daniel Á. G. <alg...@gm...>]

Hi Parker,

if you are using a mol2 file to define the receptor, rDock will read all
atomic information (including residue name and atom names) but will pay
special attention to the assigned Tripos atom types. As long as they are
correct for your modified residue atoms, it should work just fine with any
residue name. If your modified residue is charged (as I guess is the case),
things get a little more tricky:

In the full documentation section *9.1 Atomic properties* through
section *9.3 Parsing
a MOL2 file * (
http://rdock.sourceforge.net/wp-content/uploads/2014/06/rDock_User_Guide.pdf
) you will find that rDock does not read/use partial charges. So, no need
to worry about partial charges parameterization at all!  Instead, rDock
calculates formal charges for non-neutral residues (e.g. ASP residue will
have a total -1 charge divided into -0.5 assigned to each OD oxygen). And
here it comes the trick: When your modified residue bears any formal
charge, you will need to modify the lookup table to let rDock know! If you
don't do that, the residue will be neutral.

Find in section *9.5 Assigning distributed formal charges to the receptor * the
documentation about this issue. The solution is simple: you just need to
modify $RBT_ROOT/data/sf/RbtIonicAtoms.prm file to tell rDock that your
residuename XXX has a formal charge and how it is distributed among the
atoms. There is no information about the file format in the documentation,
but you will see it is pretty easy to understand and modify.

Summing up, if you have a neutral modified residue, making sure the
assigned tripos types in the input mol2 file are correct will do it. If the
residue is charged, modify the RbtIonicAtoms.prm lookup table to let rDock
know about the formal charge distribution within the residue atoms.

If you have any problem with the lookup table file format, write back ;)

Cheers!

Daniel



2015-02-21 17:27 GMT+01:00 Parker de Waal <Par...@va...>:

> Hi all,
>
> Does anyone m know how rDock handles modified residues?
>
> I'm working with a protein that is phosphorylated in the ligand binding
> pocket, however I can't find any documentation in the manual regarding
> residues such as this.
>
> Also, does rDock read charges from the mol2 receptor files? If this is the
> case I could apply charges from AMBER parameterization.
>
> Best,
> Parker
>
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-- 
Daniel Álvarez | PhD Student
dan...@ub...  | www.ub.edu/cbdd
Computational Biology and Drug Discovery Group
Faculty of Pharmacy | University of Barcelona