AMBER Archive (2007)

Subject: Re: AMBER: Known residue, unknown error in teLeap

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 17 2007 - 11:49:41 CDT

On Tue, Jul 17, 2007, Neelanjana Sengupta wrote:

> 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
> OK.
>
> 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>

I think you will have to post your pdb file...it's not clear without that
why LEaP thinks that the proline is a C-terminal residue.

Also, try making ACE-PRO-NME, with the standard NME residue. If that works,
you can look for the differences between NME and your NH2 residue (other than
the missing methyl group!) that might explain the different behavior.

...good luck...dac

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