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
atoms.
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,
Majid
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