[Chimera-users] Fwd: Pruning pdb graphically

Francesco Pietra chiendarret at gmail.com
Tue Oct 21 13:39:17 PDT 2008

Hi Elaine:
While jogging I realized that Amber still relies on TER lines, while
it still snobs HETATM. What is not comprised between two TER lines is
not considered together. So, there is an idiosyncrasy between Amber
and Chimera that must be corrected any time that Chimera saves pdb.
With my present files, as Chimera considers certain residues as
HETATM,  there is no way to renumber atoms while including TER lines
in the numbering. If you plan to implement an "amberprep" I suggest
making optional to not delete TER lines to let users on transit to
Amber (or DOCK) make hand editing.


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, Oct 21, 2008 at 6:08 PM
Subject: Fwd: [Chimera-users] Pruning pdb graphically
To: chimera <chimera-users at cgl.ucsf.edu>

Hi Elaine:
LEaP does not understand capping, with a pdb file that Chimera
understands perfectly. I have asked for light at both the Amber and
Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H
to the terminal/beginning and OXT to the terminal/last. Moreover, it
tries to join the first ACE with last NME. I have not tried separating
the capping residue with TER.


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, Oct 21, 2008 at 10:34 AM
Subject: Re: [Chimera-users] Pruning pdb graphically
To: Elaine Meng <meng at cgl.ucsf.edu>

Hi Elaine:
I had fully protonated histidine and left the chain amino group of
lysine in basic form! No excuse for that.

Now the charge is 5.0000 so that I expect that dockprep (avoiding
add-h!) will work. In my (brief) experience, Chimera is  an excellent
tool also for capping, especially if Add-H is revised for the cases of
capped residues. In some cases (12 residues capped in my case)  that
is important. Also because I want to run MD under various pH
conditions, so that capping will change (constant pH MD is not
possible with Amber under explicit medium conditions).

That Amber has updated to PDB rules is good news. Perhaps I was so
suspicious because a few days ago I found a bug with the latest
version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop):
the N-hydrogen names for LEU as first residue are written incorrectly.
A revised ambpdb is forthcoming.


On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> After looking at more parameter files, I now believe that Amber and PDB atom
> names in standard residues, including hydrogens, are the same.  My previous
> information was old (I haven't run Amber for 10 years!), sorry about that.
>  You would still need to worry about correctly naming any atoms changed or
> added with Build Structure, though.
> Besides the Amber *lib files mentioned before, you can also look up the
> standard atom names in the links from this PDB page:
> http://remediation.wwpdb.org/downloads.html
> Elaine
> On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote:
>> I forgot to mention that usually you don't need to worry about the atom
>> names, as Add Charge knows which PDB names go with which Amber
>> names/charges, and AddH uses the standard names.
>> I think you only have to worry about the names of atoms that were changed
>> or added "manually" in Build Structure, and if the nonhydrogen atoms have
>> the standard names (PDB = Amber for nonhydrogen atoms in standard residues),
>> AddH will use correct names for the hydrogens later added to those atoms.
>>  If you use hydrogens added by Build Structure, however, you have to fix
>> their names.
>> Elaine

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