AMBER Archive (2009)

Subject: Re: [AMBER] Could not find angle parameter

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Fri Apr 03 2009 - 05:58:47 CDT

Hi Quan,

Take a look at this
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig,
bottom of the page.

Marius

2009/4/3 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!
>
> quan
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