Hi,all,
Recently,I have minimized the protein-ligand complex with two
steps.Firstly, only hydrogens of the complex are minimized. Then minimize
the whole system of the complex. These two steps are done successfully. And
the potential energies have been converged. But when I load the minimized
pdb file and check it, I find some bond lengths are very short and are not
reasonable. For example,
Warning: Close contact of 0.319169 angstroms between .R<PHE 79>.A<HD2 18>
and .R<GLN 200>.A<HE22 15>
Warning: Close contact of 0.536569 angstroms between .R<ILE 105>.A<O 19>
and .R<LYS 106>.A<HG3 10>
Warning: Close contact of 0.164291 angstroms between .R<LYS 106>.A<HA 4>
and .R<LYS 106>.A<N 1>
Warning: Close contact of 0.503291 angstroms between .R<HIE 127>.A<ND1 9>
and .R<HIE 412>.A<HE2 13>
Warning: Close contact of 0.157410 angstroms between .R<ARG 177>.A<HA 4>
and .R<ARG 177>.A<N 1>
Warning: Close contact of 0.154235 angstroms between .R<NLYS 192>.A<HA 6>
and .R<NLYS 192>.A<N 1>
Warning: Close contact of 0.320126 angstroms between .R<GLU 241>.A<HG2 9>
and .R<ASP 242>.A<H 2>
I don't know why these bond lengths aren't still reasonable after
minimisation. Thanks for any suggestion.
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Received on Mon Apr 18 2005 - 11:53:00 PDT
