Greatings!
I'm facing the problem with my second step of minimization protocol.
During this step water and ions move (NTP, 300K), all atoms of protein
and ligand being restrained at 10 kcal/mol-A^2. Previous step was
minimizing only the water and ions, restraining the heavy atoms of
protein and ligands at constant 3 kcal/mol-A^2, and this step went
smooth. But when it came to the step 2 just at the very moment I got an
error message
7: 6935 - 6934 and 8: 6936 - 6934
Hydrogen atom 6934 appears to have multiple bonds to atoms 6935 and 6934
which is illegal for SHAKEH.
7: 6935 - 6934 and 9: 6937 - 6934
Hydrogen atom 6934 appears to have multiple bonds to atoms 6935 and 6934
which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
The problem is that atom 6934 is not a hydrogen at all, it is the CB
atom of ALA sidechain. Hydrogens are 6933 and 6935-6937, which indeed
have bonds with C 6934. I checked .rst file from the first step but
found no discrepancies or suspicious data. What can be the origin of my
problem?
Thank you!
--
С уважением,
Александр Злобин
группа 102 ФББ
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Received on Sat Mar 12 2016 - 07:00:03 PST
