AMBER Archive (2002)

Subject: Re: Some error message on Leap

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 10 2002 - 17:22:51 CDT

Hi Sichun,

That is not an error message, it's just that leap is telling you what your
terminal residues are, in this case your C-terminal is a proline residue
while the N-terminal is a methionine.
So if you have a structure made out of a single fragment this message is
fine. If your structure has more fragments/chains then it is wrong, the
number for C and N non-labeled terminal residues should equal the number
of fragments in your structure.

I had the same problem initially working with my structure.

Ioana

PS. See also the tutorial on "Simple free energy example" (which I also
found after asking the question, of course :) )

http://www.amber.ucsf.edu/amber/tutorial/gibbs_box/HTML/xleap_solvatesave.html

On Thu, 10 Oct 2002, Sichun Yang wrote:

> When I add protons to the PDB file by the protonate program.
> Then run tleap and give me some error messages as follows.
> Any suggestion?
>
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CPRO 1
> NMET 1
> )
> (no restraints)
>
>
>