I am interested to know how to model graphene oxide structure and use it for investigating interaction with proteins ,
make topology of standard GO as can be found for example in this publication,
http://pubs.acs.org/doi/suppl/10.1021/acs.jpcc.5b07345/suppl_file/jp5b07345_si_004.pdf
the functional groups should have order and the oxygen to carbon ratio also is important
I have used VMD to build Graphene 10 nm x 7 nm size , because the graphene sheets are usually larger than proteins
so my questions are ;
how to modify the graphene sheet obtained by vmd automatically or how to change the pdb file to obtain the topology file for simulation with OPLS force field
there is a small file generated by vega zz as I found on mailing list which is attached, is it possible to repeat it to larger size?
warmest regards
Obtaining a new topology is not an easy task, because your topology must be based on parameters compatible with the force field you intend to use, and the file format (how you store the FF information in a document), must conform to the simulation package you intend to use.
Perhaps the easiest way to obtain an acceptable and reliable topology is with the use of the AmberTools package (http://ambermd.org/), which is intended to be used with the AMBER family of force fields, but there are similar tools to build topologies for other simulation packages and force fields. To obtain a reliable topology, you will need RESP atom changer calculated with DFT BLYP3 6-31g. You may have a look at this tutorial as example:
http://ambermd.org/antechamber/efz.html
VMD is a visualization package, it dows not build topologies, but it is associated to plugins, such as psfgen, equiped to build CHARMM topologies for proteins or nucleic acids. There are also servers for lipid membrane topologies, for amber, gromacs or CHARMM. You may use VMD however, to inspect your molecules as it is able to measure bond distances, angles, and dihedrals proper and improper.
The reference you sent has actually everything you need to build the topology manually, but each simulation package has its own syntax and you should refer to the documentation on each site.
If you are using GROMACS as simulation package, the site ATB has some topologies dealing with planar graphene sheets (https://atb.uq.edu.au/molecule.py?molid=8099), which may help you to build your own topology. Actually, ATB may build the topology for you if the molecule is not too big, but only for the GROMOS force-field family.
Best wishes,
Rogelio
Thanks Yang Wang , for the update.
Just be aware, the geometry and changes were obtained with semiempirical methods. If someone wants to obtained more sounding topologies based on QM methods with a deeper level of theory, he can do it by submitting a QM optimized geometry to the ATB server.
Best wishes,
Rogelio
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