Re: [AMBER] Assigning atom type.

From: Jason Swails <>
Date: Sun, 15 Sep 2013 00:09:22 -0400

On Fri, Sep 13, 2013 at 9:52 AM, Sanjib Paul <> wrote:

> Dear Amber Users and Developers,
> I am working on carbon nanotubes.
> At first when I worked on 6:6 CNT of about 15 angstrom length, then I
> assigned atom type of 144 carbon atoms one by one by xleap. Now I want to
> assign atom type of about 50 angstrom long 6:6 CNT, which have 504 atoms.
> Assigning atom type one by one by xleap a tedious process. Is there any
> alternative way by which I can assign atom type of this 504 atoms easily?

If you have some sort of library file (mol2, Amber prep, or OFF library
file) that you generated at some stage, then the atom types are read
directly from that file.

If you have an input PDB file, you can use something like OpenBabel to
generate a mol2 file and then use a script (or just a text editor with a
clever macro) to modify the atom types in the resulting mol2 file. (Note,
you will still have to assign the charges somehow).

It would help us if we knew what you were actually doing (and, as usual, we
need the exact commands, their sequence, and any error messages you get as
well as the relevant input files).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Sep 14 2013 - 21:30:03 PDT
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