AMBER Archive (2009)

Subject: Re: [AMBER] methyl group at the N-terminal

• Previous message: David A. Case: "Re: [AMBER] 2 restraints with different force constants"
• In reply to: Francesca Poletti: "[AMBER] methyl group at the N-terminal"
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Dear Francesca,

> I would like to know whether it is possible or not to substitute one
> of the hydrogen at the N-terminal of a protein with a CH3 group
> using leap, and eventually how.

You will have to develop a new fragment for your (+)MeNH2-terminal aminoacid.

You could try to follow what is done @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
  and
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
replacing (+)NH3-Me (methylammonium) by (+)MeNH2-Me to see if this works.

regards, Francois

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• Previous message: David A. Case: "Re: [AMBER] 2 restraints with different force constants"
• In reply to: Francesca Poletti: "[AMBER] methyl group at the N-terminal"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]