Re: [AMBER] Tleap is making C instaed of Cl

From: Thakur, Abhishek <>
Date: Thu, 2 Feb 2017 17:46:30 +0000

I am bit confused,

As when I have input pdb file it had CL1 denotation for Chlorine atoms and in library file it has given me output as Cl1.

Is it obvious?

The I was playing around with my ligand containing chlorine and found that changing CL1 to CL or Cl removes the green, it is green as long it is Cl1 or Cl1.

I my complex file I am getting Cl1, so it should be green only.

From: David Case <>
Sent: Thursday, February 2, 2017 6:37:35 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Tleap is making C instaed of Cl

On Thu, Feb 02, 2017, Thakur, Abhishek wrote:
> But after solvating the system when I am generating the complex pdb and
> viewing in chimera I cannot see green color for Chlorine, it looks like
> carbon. But when I see the atom nae it says Cl1.

Look at the PDB file you are actually loading in Chimera: does the chlorine
atom have the correct element (columns 77-78 in the ATOM line)? If not, we
would need details about how you made the PDB file. If it looks OK, it might
be a Chimera issue (although that sounds kind of unlikely).

Just take a small pdb file (say the ligand itself), and play around with
what you need to do to get Chimera to color the atom the way you want.


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Received on Thu Feb 02 2017 - 10:00:03 PST
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