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

From: Thakur, Abhishek <>
Date: Thu, 2 Feb 2017 22:22:23 +0000


 Just now I have found an example file on amber tutorial which has used tleap to make parameters for ligand containing Cl ions

I am using same structure and trying to reproduce and see if I get C or Cl,

I can observe similar trend, Cl being replaced by C.

As there is difference in frcmod file generated by both of us.

Frcmod file of tutorial is

remark goes here


ca-c3-c1 64.784 110.735 Calculated with empirical approach
c1-c1-cx 56.400 177.990 same as c1-c1-c3
c1-cx-hc 48.300 109.750 same as c1-c3-hc
c1-cx-cx 64.200 111.590 same as c1-c3-c3


ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
n -o -c -os 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c -ca-n -hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default value

Where as in my case I can see only

From: Thakur, Abhishek
Sent: Thursday, February 2, 2017 10:56:50 AM
To: AMBER Mailing List;
Subject: Re: [AMBER] Tleap is making C instaed of Cl


I have downloaded my receptor from RCSB website and have docked my ligand with autodock.

The have build complex pdb with MGLTools.

Then I have use antechamber to calculate BCC charges.

Then I have used parmchk to generated frcmod file and tleap to generate other files for ligand.

The taking library file and frcmod file of ligand with the tleap I have build complex parmtop and inpcrd file and saved solvated complex pdb.

In this file I can see that at last position there is Cl, but chimera does not change gree, neither maestro 2D visualizer shows it to be Cl.

It seems to be C, but still in pdb file there it has been outputted as Cl1.

ATOM 8320 Cl1 RRR 515 -7.533 -4.212 4.655 1.00 0.00

From: David Case <>
Sent: Thursday, February 2, 2017 9:51:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Tleap is making C instaed of Cl

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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