Re: [AMBER] atom number same as line number for cpptraj

From: Jason Swails <>
Date: Tue, 22 Jul 2014 19:12:03 -0700

On Tue, Jul 22, 2014 at 5:02 PM, newamber list <>

> Hi All
> I have a pdb file obtained from cpptraj. One common problem with pdb is
> that resid or atom number restarts after 99999. So am just wondering would
> line number be a good way of using atom number which I want should be same
> as identified by cpptraj. I want to feed some atom number to cpptraj.

​I don't understand what you mean. The atom numbering restarts after 99999
because the PDB doesn't allow more characters for the atom number field.
 Another approach is to switch to hexadecimal representation at 100000
(that is what VMD does). However, cpptraj does _not_ store atom indices in
the way that it prints them to the PDB file. The atoms are numbered from 1
to N regardless of what the "number" is in the input structure.​

The line number trick won't work because molecules are separated by TER
cards (you can see that atom number 99,000 does not land on line number
99,000 for that reason). I suggest using a different file format to output
(maybe CIF), or seeing if there is a way to use the topology file directly.

I hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 22 2014 - 19:30:02 PDT
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