[gmx-users] cgnr charge classifying

[David van der Spoel]

davood ajloo wrote:
> 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
there's quite a few people simulating CNTs with GROMACS. Ask for a 
topology from someone, or search the mailing list.
x2top should be able to give you a .top file including bonds and angles 
etc. but not charges.

> 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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-- 
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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