[Dock-fans] prepare_amber.pl with phosphorylated residues

Scott Brozell sbrozell at rci.rutgers.edu
Thu Oct 7 22:51:18 PDT 2010


Hi,

On Wed, Oct 06, 2010 at 11:28:52AM -0700, Rebekah Baskin wrote:
> 
> I want to use the command prepare_amber.pl to prepare my receptor for AMBER 
> scoring, but my protein has phosphotyrosine residues in its active site 
> (designated as PTR). These are not being recognized by the program. How can I 
> fix this so that the residue names are in an Amber readable format?

The methodology for handling this type of situation was added in 
Dock 6.2.  The general procedure is to determine how one would
recognize phosphotyrosine in Amber.  And then to add the appropriate
commands into dock6/parameters/leap/cmd/leaprc.dock.user.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreInputs

Inserting phosphotyrosine into the googggglle bar at http://ambermd.org/
finds a gem:
http://archive.ambermd.org/200707/0284.html
The "contributed parameters" url is 
http://www.pharmacy.manchester.ac.uk/bryce/amber
Parameters for both phosphotyrosine with single protonated phosphate group
and phosphotyrosine with unprotonated phosphate group are listed.

As described in general in the Amber score tutorial
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
one must ensure that the phosphotyrosine residue names in the PDB file,
you indicated PTR, match those in the Amber parameter files, Y2P for
the unprotonated one above; ie, edit your PDB and change PTR to eg, Y2P.

Add the LEaP commands into 
dock6/parameters/leap/cmd/leaprc.dock.user:
loadamberparam frmod_y2p
loadOff Y2P.off 

prepare_amber.pl should now automatically recognize phosphotyrosine.
Be sure to examine the amberize*.out and *.log files for warnings and errors.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScorePractice

scott



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