AMBER Archive (2009)
Subject: [AMBER] (no subject)
From: chenquan (chenquan508_at_hotmail.com)
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!