Re: [AMBER] cyclic peptide

From: FyD <>
Date: Tue, 14 Dec 2010 19:52:39 +0100

Dear Rossella,

> I made my model as I told you (modifying an hydrogen of ACE as to be a
> carbon), and it's ok, I set the atom type as CT and charge as 0.0000.

why to you set this charge to zero ?

> I used
> the bond command, I manually erased the hydrogens on the carbons of this
> bond (I thought they would be erased by default with the command bond, but
> it wasn't so). However, I obtained my cyclic peptide. Pdb looks good. When I
> calculate the net charge, it gives me a charge of -0.21 (the sum of the
> charges of the hydrogen i erased on NME after binding and the hydrogen I
> transformed in C on ACE whose charge I turned in 0.0000).

if you have an error of charge of -.21 it is likely that your new
molecular fragment is not correctly defined.

Please see

You will find all what you need...

regards, Francois

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Received on Tue Dec 14 2010 - 11:00:02 PST
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