Re: [gmx-users] Questions regarding converting .GRO files to .TOP files
On 6/29/14, 11:46 PM, Andy Chao 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?
The .n2t file assigns bonds for any atoms that satisfy the specified distance
criteria. The error message indicates that you have some atoms that are within
bonding range of an unphysical number of bonds. Perhaps the layers are too
close together or something, but the printed atom numbers should make it very
easy to identify what is going on simply by visualizing the structure.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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Re: [gmx-users] Questions regarding converting .GRO files to .TOP files
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 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> mail to gmx-users-requ...@gromacs.org.
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