[gmx-users] topoloy for CNT

[Justin A. Lemkul]

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
>  
> COMMANDS:
> 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
> ERROR:
> .
> .
> .
> 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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