[gmx-users] Questions regarding converting .GRO files to .TOP files

[Andy Chao]

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