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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--
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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