Dear Elaine, 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. The details about the calculations are also attached in this mail along with mol2 file. Before calculation, I removed the water, oxy and so4 in het entry and did the calculations with protein and heme alone. Here is what I am getting at the end using BC-AM1 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? log file along with the charge snapshot is attached with this mail. 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 will highly appreciate your reply and suggestions. Thanks in advance, s On Nov 6, 2007 12:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi "S" We are glad you like Chimera.
(1) HEM and FE charges. AMBER charges are assigned for the protein, but not for the nonstandard residue HEM/FE. Since FE is only one atom, it will put whatever integer charge you specify on that atom (without trying to "calculate" the charge). You can see the assigned charge by labeling the atom with its charge value (see below) or looking in the charge column of the output Mol2 file, if you wrote it out. The Add Charge dialog will always show +2 for your FE because it always uses the same method to guess what the charge should be, but that does not mean the currently assigned charge is +2. I just tested this by specifying FE charge +7 and then labeling the atom; Add Charge did assign +7. For the example structure PDB 1a6m, however, +2 is the correct charge for FE and -4 the correct charge for the rest of HEM, protoporphyrin IX.
To label atoms with their charges, select the atoms of interest, then either use the commands:
labelopt info charge label sel
or use the menu Actions... Label... other... and choose the attribute "charge" from the pulldown menu in the labeling dialog.
(2) Charge set. Only all-atom charges can be assigned by Chimera, not united-atom (where the nonpolar CH CH2 and CH3 are treated as single points).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Nov 6, 2007, at 7:58 AM, snoze pa wrote:
Hi, I am new in this mailing list but found chimera more useful than any other software. I was building a protein that contain HEME. When I was calculating the charge using chimera interface, then it is asking for HEM[FE] and HEM[nonFE] formal charge. I know chimera is using MMTK and AMBER forcefield. If I will give the default value then it is assigning +2 charge to Fe, which is not a match based on AMBER forcefield. Meanwhile I try to change the Formal charge manually, but still it gives the same +2 for Fe. Anybody used chimera to prepare a protein having heme for dock or geometry build.
My another question is: Is it possible in chimera to merge nonpolar hydrogen charges on the heavy atoms, the technique used in autodock.
I will highly appreciate your help and suggestions in this matter. thanks in advance. s
