AMBER Archive (2005)

Subject: Re: AMBER: capping?

From: Heiko Meyer (heiko.meyer_at_scai.fraunhofer.de)
Date: Wed Mar 09 2005 - 11:17:01 CST

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 http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm
>See also http://www.u-picardie.fr/labo/lbpd/RED/
>Use Google @ http://amber.scripps.edu/ 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
> --
>http://www.u-picardie.fr/labo/lbpd/FyD.htm
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>
>
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.

greetings
heiko 

-- 
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
E-mail:	heiko.meyer_at_scai.fraunhofer.de
WWW:   	http://www.scai.fraunhofer.de

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