[gmx-users] Simulation of CNT with Amber forcefield

majid hasan pu_majidhasan at yahoo.com
Mon Apr 18 19:17:12 CEST 2011

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

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      ....

Thanks for your help,
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