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>_______________________________________________
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