How can I orient my protein with respect to the membrane?
GNOMM accepts pre-oriented PDB structures with respect to the membrane plane. This means that the PDB's Z- principal axis needs to be aligned to the membrane plane's normal. Such files can be retrieved from the Orientations of Proteins in the Membrane (OPM) database or the Protein Data Bank of Transmembrane Proteins (PDB-TM), or can be generated through the PPM server. Using RCSB PDB as the source of input, although available, is generally NOT recommended since the structures are not likely to have the proper orientation.
Does GNOMM accept mmCIF, GRO, CRD or other structure file formats?
No, GNOMM only uses the PDB format for both its input and its output.
Does GNOMM support other MD engines besides GROMACS?
Currently no, GNOMM supports GROMACS exclusively.
What types of force fields does GNOMM use?
GNOMM currently supports the CHARMM36 all-atom (AA), GROMOS96 54A7 United-Atom (UA), MARTINI Coarse-Grained (CG) and PACE hybrid UA/CG force fields.
What types of lipids does GNOMM support?
You can find a list of available lipids for each force field in the Lipids page.
Can the GNOMM Protein-Membrane Modeler model heteroatoms (e.g. bound ligands) or non-standard protein atoms (e.g. selenocysteines, post-translational modifications etc.)?
The GNOMM Protein-Membrane Modeler supports the submission of standard protein coordinates only. Any non-protein coordinates and non-standard atoms in the submitted PDB files are deleted.
What if I have a protein with a special modification or in complex with a special compound? Or what if I want to perform a simulation of an inorganic structure (e.g. fullerenes, carbon nanotubes?) How can I use GNOMM then?
For cases such as these, you can use the GNOMM pre-processed system Modeler, available by choosing the "Upload pre-processed PDB and topology" option in the "Submit" page. You should prepare your protein-ligand system using GROMACS in the manner that you would normally do. There is an excellent tutorial on protein/ligand simulations available in the GROMACS tutorial page, which you can use to familiarize yourself with the topic. Upload your system's structure in PDB format, its associated system topology (topol.top) and any other associated itp files to the service. GNOMM will use your supplied topology to further expand your system.
My system cannot be built, even with the pre-processed system Modeler. What can I do?
If that is the case, your system cannot be automatically handled by GNOMM. However, you can do the following: first, prepare your initial system structure and topology. Then, just build a "membrane-only" (i.e. no proteins) system with GNOMM. Finally, combine the two separate systems manually. You can do that using freely available tools such as InflateGRO, or through the "-membed" option in GROMACS's mdrun (previously known as g_membed). Again, the GROMACS tutorial page offers a really good tutorial on protein-membrane simulations, which discusses topics such as this and showcases the use of InflateGRO.
How can I use systems generated with the PACE force field?
PACE is a hybrid force field, combining a United-Atom representation for the proteins with the MARTINI Coarse-Grained force field for lipids and the solvent. This means that in addition to the standard potential energy function, a number of additional potentials are defined to model multiscaling, namely, a set of extra potentials for the phi/psi dihedral angles of the backbone, an additional function to model directionality in polar interactions and hydrogen bonds and a special, hybrid Lennard-Jones term to model non-bonded interactions between atomic and Coarse-Grained particles. These require special modifications to the GROMACS source to be operable. For this reason, compilation of tpr files with grompp requires a specially modified version of GROMACS v. 3.3.1. You can find more information on how to obtain and compile this version in the "Downloads" page.
Note that modified GROMACS 3.3.1 is required *only* for the generation of tpr files with grompp. The actual simulations can be performed with any newer version of GROMACS, including versions 4.x, 5.x, 2016.x and 2018.1.
How can I retrieve the results of my submitted job?
Upon submission, each job receives a numerical ID. You can use that job ID to check your progress and/or retrieve your results by filling the form in the Retrieve Results page.
How long does a job take to finish?
That depends on a number of factors, including the presence and size of a protein, the chosen force field, the size of the membrane and its lipid composition. The server workload can also influence the process. Typically, a system built with MARTINI will take about 5-15 min. to finish, while systems built with CHARMM or GROMOS will need more time. You are strongly advised to bookmark your job page or save your job ID to be able to retrieve your results.
How long are my results kept in the server?
GNOMM keeps all results of a job for the maximum of a month (30 days), after which they are automatically deleted.
How do I cite GNOMM in my work?
If you use GNOMM in your work, please cite the article by Baltoumas and co-workers (doi: 10.1002/jcc.25823) in the Journal of Computational Chemistry.
How does GNOMM handle my privacy and personal data?
If you use GNOMM in your work please cite:
Fotis A. Baltoumas, Stavros J. Hamodrakas & Vassiliki A. Iconomidou (2019) The Gram-Negative Outer Membrane Modeler: automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields
J. Comput. Chem.
Jul 5; 40(18): 1727-1734, DOI: 10.1002/jcc.25823