[AMBER] Re_Re: Editing residue in PDB file

From: Nikolay N. Kuzmich <nnkuzmich.gmail.com>
Date: Tue, 13 Dec 2016 17:27:10 +0300

Dear Amber users, dear David,
(whom I want to thank for the answer)

I would like to edit the pdb file manually.
The inhibitor is covalently bound with protein via serine residue.
The idea is to treat the amino acid + covalent ligand as a
single UNIT, i.e., a modified amino acid.

So I change the residue name from SER to the new one, extend it by shifting
the inhibitors atoms with their coordinates. And then some questions are

1. How/by which rules do I specify sidechain atoms in the pdb (like CA2,
HG13, N3, etc.) ?
2. The enumeration order of the chain will shift, so should I change the
atom numbers of the following residues manually (hundreds and thousands!),
or can be done automaticlly somehow?

Thank you in advance,

Message: 25
Date: Mon, 12 Dec 2016 11:17:50 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Editing residue in PDB file
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20161212161750.ywobkgdytqsyzk3z.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

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

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
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 Tue Dec 13 2016 - 06:30:06 PST
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