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

From: David Case <>
Date: Thu, 2 Feb 2017 15:51:31 -0500

On Thu, Feb 02, 2017, Thakur, Abhishek wrote:
> 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.

I too am confused: are you talking about the Atom name (in columns 13-16)
or the element (in columns 77-78)?

I don't think that you have told use exactly how you converted the "input pdb
file" into a "library file".

Second, when you refer to the "input pdb file", input to what? Is this what
you are inputting to tleap, or the file you are inputting to Chimera?

Just to repeat what I asked earlier:

> 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).


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Received on Thu Feb 02 2017 - 13:00:04 PST
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