Re: AMBER: Known residue, unknown error in teLeap

From: Neelanjana Sengupta <>
Date: Tue, 17 Jul 2007 09:33:39 -0700

This is again regarding AcProNH2 (acetyl proline amide).

Now I have successfully made a .lib file for my NH2 residue, and numbered
and renamed my .pdb file to have ACE (res#1), PRO (res#2) and NH2 (res#3).
When I load leaprc.ff02 followed by my nh2.lib into Leap, everything looks

The issues:
1) When I next load my .pdb file, Leap still adds an O- to the PROline,
thinking it to be the last residue:
Added missing heavy atom: .R<CPRO 5>.A<OXT 15>

2) I try to create bonds between C (or PRO) and N (of NH2):

> bond 1AN.2.C 1AN.3.N

and the error I get:
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
My questions:
1) How can I get rid of the additional OXT tagged to my system? I am using
2) The 'bond' command is in accordance with Ross Walker's Tutorial 4/Section
3 (the Cu atom residue). Why does it not work here? How can I get it to work
(in teLeap)?

Thanks in advance,

On 7/16/07, David A. Case <> wrote:
> On Mon, Jul 16, 2007, Neelanjana Sengupta wrote:
> >
> > 2 residues had naming problems.
> > Residues split, so res numbers will not correspond to pdb.
> This usally means that you had a set of atoms that were all in residue
> "n",
> but these atoms did not all have the same residue name. LEaP tries to
> figure
> out a decent solution to this problem, but you are better off fixing the
> pdb
> file, so that residue names and numbers are consistent.
> > Created a new atom named: H2 within residue: .R<NME 1>
> > Added missing heavy atom: .R<NME 1>.A<CH3 3>
> This is quite odd: NME is a C-terminal residue, but you seem to have NME
> as the first residue in the protein. I don't see how this can work.
> > Added missing heavy atom: .R<CPRO 3>.A<OXT 15>
> "CPRO" just means a C-terminal proline, that is, it thinks that PRO is the
> last residue in the protein. It sounds like this is not what you want.
> Again, the fix is to edit the input pdb file so that is really what you
> want
> it to be.
> ...good luck....dac
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Received on Wed Jul 18 2007 - 06:07:46 PDT
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