[Dock-fans] cofactors in dock

Scott Brozell sbrozell at rci.rutgers.edu
Thu May 17 12:50:40 PDT 2012


Hi,

On Wed, May 16, 2012 at 03:22:11PM +0530, Mary Varughese wrote:
> I have to include the cofactor GTP as part of my receptor protein and dock
> with a ligand. But chimera is not allowing to prepare rec_charged.mol2 file
> since it fails at finding amibcc charge method for GTP residue. Then i
> separately prepared the mol2 file for GTP (using gtp.prep and gtp.frcmod)
> and after performing dockprep on the receptor i opened the GTP.mol2 file in
> the same window and write the mol2 file. but again at grid generation it
> fails "Reading in coordinates of receptor.
> WARNING assign_vdw_labels: Atom valence violated for 1SA0.pdb (combined)
> **** GTP 848 C8 13145.
> Error reading in receptor."

Which version of chimera are you using ?
There was some recent activity for GTP but using Gasteiger charges:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006846.html

Are you saying that you ran antechamber separately from chimera
and got the am1bcc charges for gtp ?

scott



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