[AMBER] problem with ester bond between side chains

From: <moitrayee.mbu.iisc.ernet.in>
Date: Tue, 10 Jan 2012 16:03:17 +0530 (IST)

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
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