addH: Weird results
Hi everybody, For several months I have been saving docking results from Autodock, adding hydrogens and submitting them to Amber for molecular dynamics. Chimera worked perfectly well. A typical result is attached as <file1.pdb>. I repeated the process with a different pose of the same ligand and got very weird results. In fact the atoms were numbered differently and some atoms were not numbered at all, or rather they were given ***. I submitted some of the original ligands, that is the ligands to which Chimera added Hs correctly. A typical example is attached <docking.result_8_2.pdb>. The result of <file1.pdb> was not reproduced. The errors described above were repeated (see <file2.pdb>). Trying to renumber the atoms according to <file1.pdb> did not help. I am a bit baffled by this. Any help will be most welcome. Best regards George PS. The submitted ligand is bisabolol.
Hi again, My guess is that addH in Chimera 1.6 and above is bugged. Chimera 1.5.3 worked as expected on the same files that I sent earlier. Have a good Sunday George On Jun 10, 2012, at 12:23 PM, George Tzotzos wrote:
Hi everybody,
For several months I have been saving docking results from Autodock, adding hydrogens and submitting them to Amber for molecular dynamics.
Chimera worked perfectly well. A typical result is attached as <file1.pdb>.
I repeated the process with a different pose of the same ligand and got very weird results. In fact the atoms were numbered differently and some atoms were not numbered at all, or rather they were given ***.
I submitted some of the original ligands, that is the ligands to which Chimera added Hs correctly. A typical example is attached <docking.result_8_2.pdb>. The result of <file1.pdb> was not reproduced. The errors described above were repeated (see <file2.pdb>). Trying to renumber the atoms according to <file1.pdb> did not help.
I am a bit baffled by this. Any help will be most welcome.
Best regards
George
PS. The submitted ligand is bisabolol.
<docking.result_8_2.pdb><file1.pdb><file2.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi George, Chimera 1.6.1 is giving some of the added hydrogens 5-character atom names, which is wider that the allowed field width for atom names in PDB files and therefore the field gets filled with asterisks. I will try to get this fixed soon and will send mail again when it is. The fix will only be in the daily build though, unless and until we make a 1.6.2 build. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 10, 2012, at 3:23 AM, George Tzotzos wrote:
Hi everybody,
For several months I have been saving docking results from Autodock, adding hydrogens and submitting them to Amber for molecular dynamics.
Chimera worked perfectly well. A typical result is attached as <file1.pdb>.
I repeated the process with a different pose of the same ligand and got very weird results. In fact the atoms were numbered differently and some atoms were not numbered at all, or rather they were given ***.
I submitted some of the original ligands, that is the ligands to which Chimera added Hs correctly. A typical example is attached <docking.result_8_2.pdb>. The result of <file1.pdb> was not reproduced. The errors described above were repeated (see <file2.pdb>). Trying to renumber the atoms according to <file1.pdb> did not help.
I am a bit baffled by this. Any help will be most welcome.
Best regards
George
PS. The submitted ligand is bisabolol.
<docking.result_8_2.pdb><file1.pdb><file2.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi George, I've committed a fix for this now. It will be in the next daily build. --Eric On Jun 11, 2012, at 10:01 AM, Eric Pettersen wrote:
Hi George, Chimera 1.6.1 is giving some of the added hydrogens 5-character atom names, which is wider that the allowed field width for atom names in PDB files and therefore the field gets filled with asterisks. I will try to get this fixed soon and will send mail again when it is. The fix will only be in the daily build though, unless and until we make a 1.6.2 build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 10, 2012, at 3:23 AM, George Tzotzos wrote:
Hi everybody,
For several months I have been saving docking results from Autodock, adding hydrogens and submitting them to Amber for molecular dynamics.
Chimera worked perfectly well. A typical result is attached as <file1.pdb>.
I repeated the process with a different pose of the same ligand and got very weird results. In fact the atoms were numbered differently and some atoms were not numbered at all, or rather they were given ***.
I submitted some of the original ligands, that is the ligands to which Chimera added Hs correctly. A typical example is attached <docking.result_8_2.pdb>. The result of <file1.pdb> was not reproduced. The errors described above were repeated (see <file2.pdb>). Trying to renumber the atoms according to <file1.pdb> did not help.
I am a bit baffled by this. Any help will be most welcome.
Best regards
George
PS. The submitted ligand is bisabolol.
<docking.result_8_2.pdb><file1.pdb><file2.pdb>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
George Tzotzos