[gmx-users] x2top error in CNT simulation

[David van der Spoel]

Hero wrote:
> Dear All,
> 
> I am trying to simulate water flow in CNT and just followed the website:
> http://cs86.com/CNSE/SWNT.htm
> 
> I did the following:
> 
> 1. ffgmx.n2t
> **** must change this files name to ffencadv.n2t and add the following 2 lines:
> C C 1 C ; CNT Carbon with one bond
> C C 2 C C ; CNT double bonded Carbon
> 
> 2. ffgmxbon.itp
> add the following line to it:
> 
> #####################################
> [ bondtypes ]
> ; i j func b0 kb
> C C 1 0.14210 478900.
> #####################################
> [ angletypes ]
> ; i j k func th0 cth
> C C C 1 120.000 397.480
> #####################################
> [ dihedraltypes ]
> ; i l func q0 cq
> C C 1 0.000 167.360
> #####################################
> 
> But when I ran:
> x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
> 
> Error message appeared:
> 
> Can not find forcefield for atom C-143 with 2 bonds
> Can not find forcefield for atom C-144 with 2 bonds
> 
> -------------------------------------------------------
> Program x2top, VERSION 3.3.3
> Source code file: x2top.c, line: 206
> 
> Fatal error:
> Could only find a forcefield type for 0 out of 144 atoms
> -------------------------------------------------------
> Could you please tell me what is the problem?

x2top -pbc
where are these atoms, on the edge of the CNT? Is your box size correct 
such that you have a periodic CNT?



> 
> Thank you very much!
> 
> Jue
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se