can anyone please help me in guiding how to generate distance restraints between metal ions and its coordinating protein chain residues in gromacs.
If i make index groups of my metal ions and use genrestr -disre, it gives me distance restraints for each metal ion with the another metal ion but this is not what I want.
since i want to get the distance restraints of all the metal ions with their corresponding coordinating residues in the protein chain.
kindly help.
Thankyou in advance.
HI,
I dont know if this could help you, how about using a Flat-bottomed position restraints? You could define maybe a cylinder or a geometry that fits to your problem and it is possible to invert the restrained region with the unrestrained region, leading to a potential that acts to keep the particle outside of the volume defined.
hope this helps, Andrés
There should only be a few ligating atoms per metal ion. It should be straightforward to simply write them manually in the topology.
In theory, a merged [moleculetype] with a suitable index group should work, though you will have to inspect the results as the restraints may be assigned a bit crudely, e.g. too many atoms are included in the restraints.
Coordinate file format is irrelevant. Topological organization is most important.
Use whichever one matches the topology. A restraint directive must match the numbering of the [moleculetype] to which it belongs.
Following what Justin said you need to use the GRO or PDB file for the ions (or species you want to be restrained) and not for all your system. If you look at, the restraint will be applied following the numbering of the [ moleculetype ]. If you want to define a restraint between ions and the protein then you need to have in the same restraint directive both species in a sequence. The atom numbering in the PDB file for the system doesn't matter for the restraint.
Hello,
Did you fix it? I'm facing the same problem now. Could you please give some advice?
Thanks
Write the ions atom information to the protein gro file. Then use make_ndx to generate index files for the ions and the adjacent residues. After that, generate a distance restrain using genrestr -disre. This may help.
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