[Chimera-users] Fwd: carbon-chlorine bond

Francesco Pietra chiendarret at gmail.com
Tue Nov 18 00:18:13 PST 2008

In the fear that docking and MD had been carried out with C in place
of Cl for the ligand, I checked all. OK, correct for Cl.

I noticed that when all atom names are left-justifies in column 13,
Chimera reports the structures correctly.When all atom names are
left-justified in column 14, Chimera does not report Cl correctly.

I  writing pdb files, the various programs in DOCK/Amber are not well
consistent (although I did not carry out a thorough search). Dock6
writes the final pose pdb for receptor+ligand by left-justifying all
atom names in column 13. Amber behaves differently according to which
internal program is used.


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Mon, Nov 17, 2008 at 10:58 PM
Subject: Re: [Chimera-users] carbon-chlorine bond
To: Elaine Meng <meng at cgl.ucsf.edu>

Hi Eleaine:
Thanks. Moving Cl to columns 13 and 14, the C-Cl bond is displayed for
me too.Living with the new and the old. It will be so for quite a long

On Mon, Nov 17, 2008 at 7:46 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> I was going to write back that your PDB file from AMBER has the atom names
> mis-aligned so that Chimera probably thinks the chloride is a carbon, which
> would have a shorter automatic bond cutoff.  However, when I put those 4
> lines from your message below in a file and open it in Chimera, the elements
> are correctly identified and there is already a C-Cl bond; only the H is
> unconnected.  Perhaps the characters on the far right were sufficient to
> identify element Cl.  The H is far away and must be bonded to something else
> in the complete structure.
> Elaine
> On Nov 17, 2008, at 10:19 AM, Francesco Pietra wrote:
>> Hi Elaine:
>> Yes, it is a pdb file written with program ptraj (Amber) for the
>> minimum energy. The chlorine atom is defined as (partial block):
>> ATOM  14544 H1   AA1   341      76.488  57.341  49.169
>>  hn
>> ATOM  14545 C3   AA1   341      75.036  56.270  51.132
>>  ca
>> ATOM  14546 Cl   AA1   341      73.973  56.486  49.780
>>  cl
>> ATOM  14547 N1   AA1   341      74.619  55.535  52.192
>>  nb
>> and there are no CONECT. As you said above, prmtop/mdcrd with movie do
>> show a line connecting C-Cl, but I don't know if there is another way
>> to extract the minimum-energy structure than that pdb file.
>> Why are all other bonds shown correctly by Chimera in the above
>> situation? Why just C-Cl not?
>> francesco

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