[gmx-users] Re: x2top error in CNT simulation (David van der Spoel)

[David van der Spoel]

Hero wrote:
> Dear Gromacs,
> 
> Actually, the error is for all the 144 atoms on SWNT_6_6_144:
> 
> 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-1 with 2 bonds
> .....
> Can not find forcefield for atom C-143 with 2 bonds
> Can not find forcefield for atom C-144 with 2 bonds
>  -------------------------------------------------------

SHouldn't the carbons have three bonds? Is your input file really ok?


> 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? Suppose this code should work 
> without any problems since it has been on web for a long while.
> 
> Or problems showed up after Gromacs 3.3?
> 
> Thanks a lot!
> 
> Jue
> 
>> 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?
> 
> 
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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