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

Justin Lemkul jalemkul at vt.edu
Wed Nov 2 12:41:05 CET 2016

On 11/1/16 8:44 AM, Kamps, M. wrote:
> 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
> <http://www.gromacs.org/Documentation/File_Formats/Topology_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?

x2top is the only GROMACS tool that will be of any use here.  You will have to 
write a suitable .n2t file (see the manual) for whatever species you're dealing 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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