[gmx-users] CNT Potassium doping with GROMACS
georgea at ece.ubc.ca
Sat May 12 03:52:43 CEST 2007
Another point: is it possible to use pdb2gmx to do the job instead of
x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the
doping by potassium is in vacuum), but i got the error"Residue 'CNT' not
found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in
the /share/top folder and defined it as '[CNT]
C C 0 0'
but still get the same error.
Your help is much appreciated,
Thank you in advance,
George Abadir wrote:
> I want to make a simulation of CNT in an environment of potassium
> atoms to see how they will be adsorbed on the CNT surface (this is a
> way of doping carbon nanotubes). I built a .pdb file with a CNT and
> some potassium atoms with random coordinates around the nanotube. When
> I run x2top to have my topology file, I get the error:"No forcefield
> type for atom K with 0 bond". The problem is that the atoms of
> potassium should indeed be not bonded to anything at the beginning of
> the simulation. Does anybody have a way to describe such a system and
> avoid this error?
> Thank you very much in advance,
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