Hi all:
I would like to perform the MD simulation of ubiquitin dimer (PDB ID:
1AAR). In this dimer molecule, the K48 in one molecule form the peptide
linkage with the C-terminal of the other one.
As you known, tleap will add H-atoms automatically when I load PDB file.
As a result, three H-atoms will added to the NZ atom which form the peptide
linkage in K48. One of these H-atom will overlap with the carbon atom in
C-terminal. Such overlap will make the peptide linkage break in very short
time during the simulation.
How can I deal with such problem? Can I prevent the tleap to add H-atoms
automatically, or how to delete atoms from inpcrd and prmtop files?
The attached files are native pdb file downloaded from PDB database and
the generated pdb file after tleap separately.
Thank you!
Best Regards!
Your sincerely:
Zhou Gong
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Received on Fri May 04 2012 - 08:00:03 PDT
