[gmx-users] Re: CNT

Hero cjt0610 at yahoo.com
Tue Apr 22 05:26:33 CEST 2008

Hello, when I follow  http://cs86.com/CNSE/SWNT.htm and ran:

x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top               -r SWNT_6_6_144.rtp

I got the following message:

Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds

Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206

Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
Could you please tell me what is the problem?

Thank you very much!


Message: 4
Date: Mon, 21 Apr 2008 13:21:12 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] CNT
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1208798472.480ccd082c263 at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1

Quoting Hero <cjt0610 at yahoo.com>:

> Hello,
> I plan  to insert water molecules into a Single Wall NanoTube,
> I have generated the structure file of SWNT, but when I use:
>    pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro
> to form the gro file, I got the following error:
>    Fatal error:
>    Residue 'UNK' not found in residue topology database

pdb2gmx is not magic; see here:


There is also a very detailed link about CNT preparation that was provided to
you earlier across this list:



> Could you please help me out?
> Thank you very much!
> Jue

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