Re: N-terminal and C-terminal hydrogens

From: Michael Cooney <>
Date: Thu 12 Apr 2001 16:55:06 -0400 (EDT)


In my copy of xleap there are built-in n-terminal and c-terminal residue
types, e.g. NLYS and CARG. You could look for these N- and C- prefixes in
the residue list and see if xleap can change them. Otherwise try manually
changing the residues in the starting pdb file.

Good luck!

Michael Cooney
UGA Dept. of Biochemistry and Molecular Biology
Athens, GA 30602

On Thu, 12 Apr 2001, Troy Bothwell wrote:

> Hello all,
> I am attempting a simulation on a short peptide (5 amino acids). However
> when I build the molecule in LEAP, it leaves off both the extra n-terminal
> and c-terminal hydrogens. Using the edit mode of xleap and the "add H and
> build" command added a hydrogen to the c-terminal end, but not the
> n-terminal. So I added the missing hydrogen manually, and built the
> structure. I then used the check feature to see if these "new" residues
> would be recognized and they weren't. The n-terminal end it Tyrosine and the
> c-terminal end is Valine. Do I have to prepare a prep file to solve this
> problem.
> Troy

From Ryan.H.Lilien_at_Dartmouth.EDU 13 Apr 2001 09:41:59 EDT
Message-id: <43333006.dasher.Dartmouth.EDU>
Date: 13 Apr 2001 09:41:59 EDT
From: Ryan H. Lilien <Ryan.H.Lilien_at_Dartmouth.EDU>
To: AMBER list <>
Subject: AMBER vdW
In-Reply-to: <>

  I'm trying to implement the AMBER vdw term and am coming across missing parameters. I am using parm96.dat (or parm99.dat) and am using the amino acid templates. Several atom types specified in the file are not found in the parm96.dat (or parm99.dat). Specifically the atom types N3, C*, CW, NA, CN, and CB don't have R and e values in the parm files. Since these atom types are specified in your AA-template file I'm assuming that you have parameters for them. Please advise.

Thank you,
Ryan Lilien

Department of Computer Science
Dartmouth College
Received on Thu Apr 12 2001 - 13:55:06 PDT
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