[gmx-users] cgnr charge classifying

[davood ajloo]

I want to construct the trp file for a nanotube, I used prodrg but it could not calculate for non flat sp2 carbon(nanotube) .  I used X2top to creating the top file from pdb (from Hyperchm), It only gave me the connetction, no bond and angles and others parameters. I got them from literature and put them in the top file and calculated the charge from quantum mechanics program. In topology file the charges were oredred on the cgnr group. It is on the basis of the group which sum of their charges are zero. But I dont know how I order charge for nanotube. finally how I can the topology file for carbon nanotube
  with best regards
  Ajloo

David van der Spoel <spoel at xray.bmc.uu.se> wrote:
  davood ajloo wrote:
> Dear gmx-users
> I want to classifying the charge on the basis of cgnr charge type. How I 
> do it?
please explain better what you want to do.

> Thanks a lot of
> Ajloo
> 
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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