[gmx-users] Simulation of a solid surface within Gromacs

Kamps, M. m.kamps at student.rug.nl
Tue Nov 1 13:44:45 CET 2016

Dear GMX-users,

First of all, I'm sorry if my question is a stupid one. I'm pretty new to
Gromacs and I'm trying to do my best to figure it all out.

I'm trying to work with a solid surface within Gromacs. The final goal of
my simulation is to analyse the behaviour of certain proteins on a metallic
or ceramic substrate and to find the energies related to this system. I'm
having difficulties when trying to implement a surface in Gromacs.

When I create a surface in, for instance, Avogadro or VMD Inorganic
Builder, it is possible to create a .pdb file of such a structure. However,
none of the forcefields can handle the residues, and the error: "Residue
'XXX' not found in residue topology database" arises. The User Manual gives
several options here, but I'm not sure how to approach this problem. In the
manual these options are mentioned:

*If you want a topology
<http://www.gromacs.org/Documentation/File_Formats/Topology_File> for an
arbitrary molecule, you cannot use pdb2gmx
<http://www.gromacs.org/Documentation/Gromacs_Utilities/pdb2gmx> (unless
you build the .rtp
<http://www.gromacs.org/Documentation/File_Formats/Topology_File> entry
yourself). You will have to build it by hand, or use another program (such
as x2top <http://www.gromacs.org/Documentation/Gromacs_Utilities/x2top> or
one of the scripts contributed by users
<http://www.gromacs.org/Downloads/User_contributions>) to build the .top
file <http://www.gromacs.org/Documentation/File_Formats/Topology_File>.*
*- see if there is a different name being used for the residue
<http://www.gromacs.org/Documentation/Terminology/Residue> in the residue
database <http://www.gromacs.org/Documentation/File_Formats/Topology_File>
and rename as appropriate,*

*- parameterize
<http://www.gromacs.org/Documentation/How-tos/Parameterization> the residue
/ molecule yourself (lots of work, even for an expert),*

*- find a topology file
<http://www.gromacs.org/Documentation/File_Formats/Topology_File> for the
molecule, convert it to an .itp file
<http://www.gromacs.org/Documentation/File_Formats/Topology_File> and
include it in your .top file

*- use another force field
<http://www.gromacs.org/Documentation/Terminology/Force_Fields> which has
parameters available for this,*

*- search the primary literature for publications for parameters for the
residue that are consistent with the force field that is being used*

Based on the first sentence, I cannot use pdb2gmx and therefore have to
build the topology myself. How can I do such a thing? Is there a (simple)
guide available?

Also, am I taking the right steps for creating a surface within Gromacs? Is
there a (easier) different way?

Any help is appreciated,


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