Dear GROMACS users:
I have a few questions about converting the .GRO files to .TOP files. I
first used Python to create a sheet of graphene layer by using the
following Python codes:
from ase import *
from ase.structure import graphene_nanoribbon
from ase io.import*
gnr1 = graphene_nanoribbon(8,8, type='armchair')
write('graphene.pdb', gnr1, format='pdb')
Second, I used the following codes to convert the PDB file to GRO file for
the cathode layer:
editconf -f graphene.pdb -o graphene_cathode.gro
Third, I used the following codes to convert the PDB files to GRO file for
the anode layer:
editconf -f graphene.pdb -translate 0 5.0 -o graphene_anode.gro
Fourth, I combined the cathode layer and the anode layer to one complete
structure according to the following code:
genbox -cs graphene_cathode.gro -cp graphene_anode.gro -maxsol 5000 -box 3
1 3 -o electrodes.gro
Fifth, I converted the electrode gro file to top file according to the
following code:
g_x2top -f electrodes.gro -ff cnt_oplsaa -o device.top
GROMACS showed that there are carbon atoms force field that can not be
found in the atomname2type.n2t file.
part of the error message is shown as the following:
Can not find forcefield for atom C-447 with 6 bonds
Can not find forcefield for atom C-448 with 5 bonds....
Fatal error:
Could only find a forcefield type for 364 out of 512 atoms.
My atomname2type.n2t file consists of the following:
C opls_145 -0.12 12.011 3 C 0.150 C 0.150 H 0.108
C opls_145 -0.12 12.011 3 C 0.133 C 0.150 O 0.140
C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140
C opls_145 0.0 12.011 2 C 0.140 C 0.140
However, the TOP files for the cathode layer or the anode layer can be
converted from the GRO files without any error as the following:
g_x2top -f graphene_cathode.gro -ff cnt_oplsaa -o graphene_cathode.top
g_x2top -f graphene_anode.gro -ff cnt_oplsaa -o graphene_anode.top
can people explain why? What is the reason behind the error message that I
got when converting the GRO file of two combined layer of graphene to the
TOP file while the same atomname2type.n2t file is used?
Thank you very much!
Andy
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