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
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
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
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
Hi Elaine, Thanks a lot for such a detailed reply. I higly appreciate your time. I have a last question, I hope you won't mind it. In chimera website there is a option for user specified partial charges... I spend a lot of time to use a Define attribute: but no success so far. How can I change the partial charge of FE in heme using define attribute. Once again, thank you very much for your time and help. best regards s http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h...
Dear S, I forgot to mention before that the label will not automatically change when the charge value is changed. You have to re-label to see the new charge. Just thought I would mention that first, in case that is the problem! Otherwise, you only want to change the charge of one atom? Seems like it would be easier to just edit the charge value in the Mol2 file than to use Define Attribute. Also, for one atom you could just use the "setattr" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html For example, in 1a6m the iron is :hem@fe, so if you wanted charge=1.5, the command would be: setattr a charge 1.5 :hem@fe However, in case you mean FE is just an example and you might want to change the charges of multiple atoms, I attach an example file to use with Define Attribute to define the charges of all the atoms in HEM. This plain text file assumes your structure is open as #0 and has the same HEM atom names you would get by adding hydrogens to 1a6m. You could edit the charge values and atom names as needed, then choose "Tools... Structure Analysis... Define Attribute" and then open this text file, which will set the charge values as specified (FE is 1.75, etc.). 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 P.S. If you use only the FE charge from your amber data but not the rest of the values for the HEM residue, it might not add up to the correct net charge. I'm guessing those charges were generated by considering FE and the rest of HEM together as one residue. Just something to consider, and perhaps it is not that important for your purposes. P.P.S. Some details you probably don't care about but maybe others in the list would be interested: I made this attribute definition file using the "Attribute Calculator" tool with the "Formula" set to atom.charge (i.e. I didn't calculate anything, just used the tool to write out an existing attribute), naming the attribute "charge" and specifying "Save calculation results to file." To make sure it worked, I text-edited the FE charge to 1.75 and reassigned the values with this file and "Define Attribute" as described above.
I forgot to mention one more thing about that attribute definition file. It has #0:154.het on each line, which happens to specify the HEM residue in 1a6m. You could just edit the text to replace each of those with :hem (since in your structure HEM is probably not residue number 154). The first column after the tab is just the same type of specifier you would use in the command line, so there are different possibilities that would all work. You can use the command line to make sure a specifier works, for example, select an atom with sel :hem@hab to make sure that ":hem@hab" specifies an atom in your structure. Elaine
Thanks a lot Elaine, I really appreciate your time and help. Seems like playing with metal is tricky but not difficult. Thank you. s On Nov 6, 2007 4:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I forgot to mention one more thing about that attribute definition file. It has #0:154.het on each line, which happens to specify the HEM residue in 1a6m. You could just edit the text to replace each of those with :hem (since in your structure HEM is probably not residue number 154). The first column after the tab is just the same type of specifier you would use in the command line, so there are different possibilities that would all work. You can use the command line to make sure a specifier works, for example, select an atom with sel :hem@hab to make sure that ":hem@hab" specifies an atom in your structure.
Elaine
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