[Dock-fans] cofactors in dock

Mary Varughese maryvj1985 at gmail.com
Wed May 16 02:52:11 PDT 2012


Hi,

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."

how can i solve this situation.

thanking you
-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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