Hi, I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this. The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there. Thanks, Terrance Chiang
Hi Terrance, The Chimera error means the format of the APBS potential file you are opening is wrong. Probably you are not opening the correct file or the file is empty. Below is an example what the first few lines a correct APBS potential file looks like. We do not have documentation in how to use pdb2pqr or APBS. You may be interested in Coulombic electrostatic potential calculation added to Chimera 1.4, under menu Tools / Structure & Binding Analysis. You'll need a Chimera daily build to use this. Tom # Data from APBS 0.3.2 # # POTENTIAL (kT/e) # object 1 class gridpositions counts 65 97 97 origin -8.064450e+00 -4.768105e+01 -4.266980e+01 delta 3.779047e-01 0.000000e+00 0.000000e+00 delta 0.000000e+00 4.098240e-01 0.000000e+00 delta 0.000000e+00 0.000000e+00 4.099125e-01 object 2 class gridconnections counts 65 97 97 object 3 class array type double rank 0 items 611585 data follows 8.921700e-01 9.000006e-01 9.078676e-01 9.157664e-01 9.236924e-01 9.316403e-01 9.396046e-01 9.475795e-01 9.555586e-01 ... Terrance Chiang wrote:
Hi,
I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this.
The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line
I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there.
Thanks, Terrance Chiang ------------------------------------------------------------------------
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Hi Terrance, Chimera does not read "pqr" files, such as those created by the pdb2pqr server. The "pqr" file is only input to APBS, whereas the APBS output (the electrostatic potential map) is what Chimera can read and display. I can't help with the pdb2pqr server -- that is another group's server. Were you trying to open the pqr file in Chimera? If you were really opening APBS output, however, we would need to see the file: you could use Help... Report a Bug in the Chimera menu and attach that file. APBS is a separate program, not included with Chimera. It is free but you might have to compile it yourself. This page includes links to the home pages for APBS, DelPhi, and UHBD, all programs whose electrostatic map output Chimera can read and display: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> If you would prefer not going to the effort of obtaining any of those programs and figuring out how to run them, there is a simpler option in recent versions of Chimera (need to get the daily build, version 1.4): "Coulombic Surface Coloring" (under Tools... Surface/Binding Analysis). This type of calculation is not as accurate as the continuum electrostatics calculations done by the programs mentioned above, but simpler and easier to obtain... like so many things in life, a trade-off. Here is the man page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ coulombic.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 11, 2009, at 3:34 PM, Terrance Chiang wrote:
Hi, I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this.
The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line
I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there.
Thanks, Terrance Chiang
participants (3)
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Elaine Meng -
Terrance Chiang -
Tom Goddard