Hello.
In my study, the Cys residue would attack to the ligand and form a
intermediate.
Now I would like to run a classical MD simulation for the intermediate.
Since the resulted intermediate is not a standard residue, I would like to
treat the intermediate as a CYM residue and a single ligand and then add a
bond between them.
However, since the S atom is too negative in CYM, I need to change the
charge of CYM in all_amino94.lib file.
I have modified the charge of all the sidechain atoms, and have make the
sum of the charge equal to 0.
And I also change the S in all_amino94.prep from "E" to "S", which would
allow S to form two bonds.
After that, when I run tleap, it stopped at loading the parameters of CYM.
Do I miss anything? Or any suggestion to deal with the intermediate?
Any help would be appreciated!
Thank you!
Zhihong
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Received on Wed Nov 03 2010 - 13:00:03 PDT
