George Abadir wrote:
Hi,
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,
first make a topology for the CNT with x2top, then manually add the
potassium (chapter 5).
Regards,
George
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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