[gmx-users] Carbon Nanotube Simulations

George Abadir georgea at ece.ubc.ca
Thu Mar 29 04:55:01 CEST 2007

There is no C1 and C2 atom in the input PDB file, and the topology file 
is not generated because x2top doesn't generate a topology because of 
the errors. I don't understand what C (1) and C (2) means but it is not 
C1 and C2; I mean not two different types of atoms. The PDB file is 
generated simply from tubegen and I defined the residue type in the rtp 

Mark Abraham wrote:

> George Abadir wrote:
>> Hi, thank you very much for your help.
>> I capped the CNT with hydrogen atoms (i.e., I changed the carbon 
>> atoms at the ends of the tube into hydrogen atoms), but now I get an 
>> error "No
>> forcefield type for atom C(1) with 2 bonds" instead of ""No 
>> forcefield type for atom C(2) with 1 bonds" ! Is there any way to 
>> solve this?
> Not without knowing what's wrong with the topology for C1 and C2. 
> That's your job :-)
> Mark
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