Re: [AMBER] Editing residue in PDB file

From: David A Case <>
Date: Mon, 12 Dec 2016 11:17:50 -0500

On Mon, Dec 12, 2016, Nikolay N. Kuzmich wrote:
> I am going to make simulation of a protein with covalently bound inhibitor.

This is generally a (somewhat) complicated problem. Is the amino acid to
which the ligand is bound also changed? If so, you will need to define
a UNIT for tleap for both the modified amino acid and for the (modified)
ligand. Often, it makes sense to treat the amino acid + covalent ligand as a
single UNIT, i.e., a modified amino acid.

> My inhibitor will differ from the one in original pdb file.
> How should I better edit it preserving the connectivity and avoiding
> entries in pdb file like "unknown atom", etc.?
> Is possible to do it with xLeap editor or VMD or maybe another software?
> Using Maestro and then pdb4amber led to the isolated "unknown atoms".

It's not clear what you did here, or if/how you got an entry in the the pdb
file that indicated "unknown atom".

> Or can I edit the pdb file manually as well?

You can certainly manually edit the pdb file, and this is often required.
But remember that tleap needs to have UNITs definined that exactly match (in
both residue names and atom names) the entries in the PDB file.


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Received on Mon Dec 12 2016 - 08:30:02 PST
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