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