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