Dear Amber Users,
I am doing a MD simulation that has two proteins linked by a side chain ester
bond between Ser-OH and Cys-COOH. When I use leap to generate the prmtop files,
the missing atons which forms the ester bond is added to the system by leap thus
removing the ester linkage. However, I want to retain the ester linkage during
my simulations. Any suggestion as to what I should do would be highly
appreciated.
I would eagerly look forward to the suggestions.
Many thanks and Sincere Regards,
Moitrayee
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Received on Tue Jan 10 2012 - 03:00:03 PST
