AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Apr 03 2009 - 07:17:36 CDT


On Fri, Apr 03, 2009, chenquan wrote:
>
> 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´╝Ü"Could not find angle parameter: CT - OH - C". The
> force fields I specfied is leaprc.ff03 and leaprc.glycam04EP.

There are no esters in standard amino acids, and hence no relevant
parameters in the standard parameter files. You will need to develop
your own force field parameters here. Check out tutorial B4 for one way
to begin.

>
> 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.

It's hard to help, since you give so few details of what you actually
did. My guess is that you have not yet created a unit with the ester
bond in it; this will have a special residue name (not one of the
standard names). If you use that, the bonds should remain intact.

...dac

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