Re: AMBER: capping?

From: Heiko Meyer <>
Date: Wed, 09 Mar 2005 18:17:01 +0100

FyD wrote:

>>I am doing simulations of short peptides which required to be
>>acetylated and amidated at N and C termini.
>>Is there any one here can give me some suggestions how to
>>perform capping in Amber? I would like to cap the peptides with Ace
>>and Nme. I am a new amber user. Any suggestion is appreciated. Thanks.
>Please read
>See also
>Use Google . selecting 'mailing list archives' using
>"RESP charge derivation"
>This has been numerous times discussed.
> F.-Y. Dupradeau
>DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
>The Scripps Research Institute, La Jolla, CA, USA
> --
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to
open your pdb with an editor
for the C-term replace in the last row "OXT" with "N" and the 3 letter
code of the AA to NME
fo the N-term replace in the 4th row "H3" with "C" and the 3 letter code
of the AA to ACE
then use leap to add the missing atoms.


Heiko Meyer
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin, Germany
Phone: 	+49 - (0)2241 - 14 2574
Fax:   	+49 - (0)2241 - 14 2181
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 09 2005 - 17:53:03 PST
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