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

Hero cjt0610 at yahoo.com
Tue Apr 22 18:54:40 CEST 2008


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
 -------------------------------------------------------
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?


      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ



More information about the gromacs.org_gmx-users mailing list