Re: [AMBER] Re_Re: Editing residue in PDB file

From: David A Case <>
Date: Tue, 13 Dec 2016 10:30:41 -0500

On Tue, Dec 13, 2016, Nikolay N. Kuzmich wrote:
> 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 there the inhibitors atoms with their coordinates. And then
> some questions are evolving:
> 1. How/by which rules do I specify sidechain atoms in the pdb (like CA2,
> HG13, N3, etc.) ?

You don't need to do this: pdb files don't contain that sort of information.

> 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?

I'm not sure why the chain order will change, but it should not matter: tleap
numbers the residues sequentially, starting with "1" for the first residue in
the PDB file. So as long as each new residue has a residue number different
from the previous one, you should be fine.

Notes: you will still, of course, need to constuct the library for your
serine+inhibitor combo. See tutorial B5 to help get started. Also, if you
have thousands of residues, consider trying some small test simulations
(including the inhibitor) to make sure everything seems to be working before
embarking on the full project.


AMBER mailing list
Received on Tue Dec 13 2016 - 08:00:03 PST
Custom Search