Re: [AMBER] parameter for CNTs

From: Jason Swails <>
Date: Thu, 31 Mar 2011 16:54:03 -0700

On Thu, Mar 31, 2011 at 4:02 PM, Jagur Lambix <> wrote:

> Hello All,
> I am planning to do a simulation of prot-CNT (Carbon-Nano-Tube) using
> Amber.
> I checked the structure of CNT, and set all the atoms as CA atom type (from
> parm99.dat) in my PDB file.

Atom TYPEs are not defined in the PDB file. That's just the atom name
(hence the error you get). You need a library file to provide the mapping
from atom NAMEs to atom TYPEs. I've never tried doing nanotubes before, but
the design of leap is optimized for biopolymers (proteins and nucleic acids,
for example), that can be broken up into small residues in a straightforward

Trying to do something like this with Leap will probably require a more
in-depth knowledge of how leap works in order to "trick" it into doing what
you want.

Hope this helps,

When I started to prepare the top file using leaprc.ff99SB , Leap denies to
> create the top and the message is as follows:
> > CNT=loadpdb prot-CNT.pdb
> Loading PDB file: ./prot-CNT.pdb
> -- residue 179: duplicate [ CA] atoms (total 66)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
> Unknown residue: MOL number: 178 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Added missing heavy atom: .R<MET 145>.A<CG 8>
> Creating new UNIT for residue: MOL sequence: 179
> Created a new atom named: CA within residue: .R<MOL 179>
> total atoms in file: 1605
> Leap added 1619 missing atoms according to residue templates:
> 1 Heavy
> 1618 H / lone pairs
> The file contained 1 atoms not in residue templates
> FATAL: Atom .R<MOL 179>.A<CA 1> does not have a type.
> Can anyone please help me out here, how to set the parameter for CNTs ?
> Thank you
> Jagur
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Mar 31 2011 - 17:00:02 PDT
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