Re: [AMBER] Leap adding an extra incorrect hydrogen

From: Almus <>
Date: Fri, 26 Nov 2010 12:07:12 +0100

> This is because this atom is NOT in your amber prep file (which is what you
> want, correct?). H42 is not in the amber prep file, so it is not given a
> type in the ALE residue. If you are loading a PDB with an ALE residue in
> it, that PDB likely has the H42 atom, which is not mapped to anything by the
> Amber prep file you created, thus giving this error.
> If you WANT that hydrogen atom in your system, you'll have to remake the
> amber prep file with that hydrogen. If you do NOT want that hydrogen atom
> in your system, then just remove the offending H42 from your PDB file and it
> should work just fine.

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:

 - C4A = N -

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.

Again, thank you very much for your help.

> Good luck!
> Jason

Almudena Pino
Universidad de Málaga
AMBER mailing list
Received on Fri Nov 26 2010 - 03:30:04 PST
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