[gmx-users] Simulation of CNT with Amber forcefield

majid hasan pu_majidhasan at yahoo.com
Mon Apr 18 21:27:58 CEST 2011

Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. But 
g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a different 
forcefield then I get this error: Fatal Error: No or incorrect atomname2type.n2t 
file found,
which is because other forcefields don't contain any .n2t files. And, I don't 
want to create cnt.top using oplsaa/gromos because these forcefields are not 
suitable for dna. So what is the way around i.e if I can't use the same force 
field to construct both (cnt and dna) topologies, then what do I do? 

Is any of following likely to work (though I don't think so):

1) Create cnt.top and cnt.rtp using x2top oplsaa, and add cnt.rtp in amber?
2) Add an atomname2type.n2t in amber?

Lastly, the link http://cs86.com/CNSE/SWNT.htm doesn't contain anything at the 
moment. Has it been replaced by some other link or is it permanently down? 


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Mon, April 18, 2011 10:25:39 AM
Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield

majid hasan wrote:
> Dear All,
> I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT 
>using Amber99, which has been used for such systems, and CNT atoms are modeled 
>using sp2 carbon parameters.
> But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, 
>and Amber99 forcefield, I get this error:

Have you created an .rtp entry for your CNT?  I doubt that it's even possible 
for cyclic molecules like this one.  pdb2gmx is only useful for linear molecules 
composed of repeating building blocks, with limited support for branching.  You 
may want to consult:


Some of that information is outdated, but there is a plethora of information in 
the list archive about proper CNT topology generation.  Search for posts by 
Christopher Stiles.

> Fatal Error: Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms 
>while sorting atoms.

This answers my question above.  Your structure is being interpreted as RNA. 
Without significant effort and perhaps code modification, pdb2gmx is not likely 
to be useful here.

> During the execution, it says "There are 1 chains and 0 blocks of water and 1 
>residues with 168 atoms" after analyzing pdb file.
> So I suspect problem is that it reads carbon as a residue in my .pdb file. 
> If this is the problem, then how do I make sure that it reads carbon as an atom 
>and not a residue?
> My .pdb file has entries of the form:
> ATOM  1   C     C  A   1  4.039    ....
> ATOM  2   C     C  A   1  3.97      ....

Well, you've named your residues "C" and the component atoms "C" so there's no 
real confusion about anything.  It's also not the source of your problems.

g_x2top may be a useful program for generating a topology, or perhaps other 
software that is entirely unrelated to Gromacs.


> Thanks for your help,
> Majid

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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