[gmx-users] topoloy for CNT

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 13 01:30:53 CET 2011

trevor brown wrote:
> Dear friends,
> My aim is to establish a topology for a CNT. My commands and the error 
> are below.
> Does anyone tell me what I should do?
> trevor
> editconf -f cnt.pdb -o box.gro -c -box 8.0 8.0 8.0
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> g_x2top -f box.gro -o box.top -pbc -nopairs -name cnt1 -nexcl 5
> .
> .
> .
> Can not find forcefield for atom C-1498 with 2 bonds
> Can not find forcefield for atom C-1499 with 2 bonds
> Can not find forcefield for atom C-1500 with 2 bonds
> -------------------------------------------------------
> Program g_x2top, VERSION 4.5.3
> Source code file: g_x2top.c, line: 206
> Fatal error:
> Could only find a forcefield type for 0 out of 1500 atoms

You probably have to add more definitions in the .n2t file.  g_x2top is not 
recognizing any of the atoms.  Be warned, as well, that the -pbc option may 
cause the program to hang (it did in all of the 4.0.x versions).  Bonds, angles, 
etc across periodic boundaries would thus have to be added manually.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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