On Fri, May 04, 2012, Zhou Gong wrote:
>
> 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.
Simplest(!?!) approach: load in the dimer pdb file in xleap, use the "edit"
command to get a visual window. Use the "erase" button to remove any extra
hydrogens (and the OXT atom in the C-terminal residue, if it is there),
use the "draw" command to add a bond between the N of K48 and the C-terminus,
then save the prmtop in the usual fashion.
....good luck...dac
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Received on Fri May 04 2012 - 12:00:03 PDT
