AMBER Archive (2009)

Subject: [AMBER] (no subject)

From: chenquan (chenquan508_at_hotmail.com)
Date: Fri Apr 03 2009 - 05:12:14 CDT

Dear AMBER users，

I am doing a simulation of protein. Ester bond forms between the carboxyl of one residue and hydroxy of threonine in the protein. when I run the command "saveamberparm AA cmp.prmtop cmp.inpcrd", there is always a error："Could not find angle parameter: CT - OH - C". The force fields I specfied is leaprc.ff03 and leaprc.glycam04EP.

In additon, after I load the protein and run "savepdb", the ester bond is breaked which is treated as the N-terminal and C-terminal. In fact, the bond is connected before I load it.

Can anyone please help me out? Thanks!

quan
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