Re: [AMBER] Leap adding an extra incorrect hydrogen

From: case <>
Date: Fri, 26 Nov 2010 08:29:21 -0500

On Fri, Nov 26, 2010, Almus wrote:
> Thank you very much for your answer. I am afraid I didn't explain myself
> very well before. No, H24 does not exist in the PDB file, not in the
> complex's enzyme-molecule not in the the molecule's only PDB file ,
> cause the structure is like this:
> H14
> |
> - C4A = N -
> |
> HN
> So my question was, if C4A is only bonded to one hydrogen atom in the
> PDB file, prep file assigns a correct type for it, why leap adds an
> extra hydrogen? It seems that leap is not considering the double bond
> C=N somehow. So right now, my main concern is to figure out why is this
> happening and how I can solve it.

Leap doesn't use anything related to double bonds or the like. When you get
the "adding new atom" message, it is because there is an atom in the PDB file
you are loading that is not in the library file for that residue. You need to
make sure that the atom names in the pdb file exactly match the atom names in
the residue you have loaded. You can use the "desc" command in leap to find
what atom names leap thinks are there. If you still cannot figure it out, you
may need to post a small example (both the pdb file, the library file and the
exact commands you are using).


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Received on Fri Nov 26 2010 - 06:00:04 PST
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