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

[Dr. Vitaly Chaban]

I believe x2top works nice only when you have a single molecule in a
structure file.

Perhaps, the algorithm wants to connect molecules, which are not
actually connected, and goes crazy, but it is just a guess.


Dr. Vitaly V. Chaban


On Mon, Jun 30, 2014 at 5:46 AM, Andy Chao <achao at energiaq.com> wrote:
> 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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