[gmx-users] Simulation of CNT with Amber forcefield

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube

Some of that information is outdated, but there is a plethora of information in 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.

-Justin

> Thanks for your help,
> Majid
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================