AMBER Archive (2002)

Subject: Re: Amino acid unit "NHE" problem ?

From: Raik Grunberg (raik_at_pasteur.fr)
Date: Thu Jan 17 2002 - 09:23:30 CST

I haven't tried NHE yet but NME (N-methyl amine) works.
Cheers
Raik

On Thu, 17 Jan 2002, S. Jang wrote:

|I tried to construct peptide with leap with AMBER6. I want to use acetyl
|beginning group(ACE) and amine ending group(NHE). According to the
|manual "NHE" should work fine.
|But it seems leap doesn't recognize "NHE" . Here is the message.
|_____________________________________________________________________
|protege[sjang] 1> tleap
|-I: Adding /usr/local/amber6/dat to search path.
|-I: Adding /usr/local/amber6/dat/leap/lib to search path.
|-I: Adding /usr/local/amber6/dat/leap/cmd to search path.
|
|Welcome to LEaP!
|Sourcing leaprc: /usr/local/amber6/dat/leap/cmd/leaprc
|Log file: ./leap.log
|Loading parameters: /usr/local/amber6/dat/parm94.dat
|Loading library: /usr/local/amber6/dat/leap/lib/all_nucleic94.lib
|Loading library: /usr/local/amber6/dat/leap/lib/all_amino94.lib
|Loading library: /usr/local/amber6/dat/leap/lib/all_aminoct94.lib
|Loading library: /usr/local/amber6/dat/leap/lib/all_aminont94.lib
|Loading library: /usr/local/amber6/dat/leap/lib/ions94.lib
|Loading library: /usr/local/amber6/dat/leap/lib/water.lib
|> test=Sequence{ ACE ALA ALA NHE }
|sequence: Illegal UNIT named: NHE
|>
|__________________________________________________________________
|
|Any idea how to deal with this ?
|Thank you.
|
|Soon
|
|
|

=====================================================
Raik Grünberg | Bioinformatique Structurale
                        | Institut Pasteur
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raik_at_pasteur.fr | 75015 Paris
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