On Nov 6, 2007, at 11:32 AM, snoze pa wrote:
Thank you very much for your detailed reply. I worked on the PDB id 1A6M as suggested by you and followed the same instructions. I used +2 for FE and -4 for HEME and found following message at the end.
Charges for residue HEM[non-FE] determined Total charge for #0: 2.0001 Unable to find GAFF type for #0:154.het@FE what is this message?
Don't worry about this message - GAFF type is only needed for energy- minimization in Chimera, and is not used or needed by DOCK.
So, Can I use this mol2 file in DOCK 6 calculations? I am lil worried since the pre-calculated charges for amber are different from the the one I am getting using chimera and antechamber combination.
I don't know what you mean by "precalculated charges for amber" - is there some file or online information for HEM charges you are looking at? If so, whoever made it probably used 6-31G* and RESP to get those charges, rather than Antechamber and AM1-BCC. For nonstandard residues like the HEM, you can actually use whatever charges you want, but it is a little more complicated than just using Antechamber. To get different charges in the Mol2 which you will later use in DOCK, you could either (1) just edit the output Mol2 file and change the charges or (2) run Dock Prep without writing Mol2, reassign charges, then use File... Save Mol2. For more information on reassigning charges, see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html#user-specified #1 might be easier in your situation, at least if your HEM atom names match the ones in the AMBER data you are looking at. Best Elaine