I would like to calculate the structure of a peptide+porphyrin complex. I measured 2D 1H-1H NOESY spectra of a peptide+porphyrin sample, so I have intra-NOEs of the peptide in the bound form and inter-NOEs among peptide and porphyrin hydrogens. I am wondering whether it is possible to calculate the complex structure using ARIAweb server and Analysis V3. In detail:
Can I use ChemBuild to create the porphyrin in Analysis V3 project as molecular chain? note that the porphyrin contains a zinc cation, and I would like to have it in the molecular chain of the porphyrin;
the Structure module of Analysis V3 is suitable for my complex?
do you now whether ARIAweb server is able to perform structural calculation with a molecular system containing a peptide together with an organic molecule like a porphyrin?
Yes you can use ChemBuild to create a porphyrin with a zinc cation. You can either do it “from scratch” or you can try to find it in VuisterLab GitHub page.
It is often easier to find the correct compound if you have a PDB code for it, which you can find on RCSB or Chemical Components databases.
If you search for porphyrin on RCSB you can find a pdb structure in complex with porphyrin iron (pdb code: POR), although not exactly what you are looking for it can be a good base for building/modifying molecule in ChemBuild.
Once you have compound saved as chemComp you can import it into V3 project. You should have two chains, one with your peptide and one with porphyrin Zn.
The structure module will work fine with chemComp and you should have no problem with exporting to NEF.
It is more problematic to run structure calculations though as you need a bespoke topology and parameter file describing your molecule to achieve. (You can have a look at ATB server: https://atb.uq.edu.au/)
There is an option to have “User defined” topology and parameter files in AriaWeb, but I suspect it is quite a difficult job. Maybe Aria mailing list would be a source of help with that: https://listes.services.cnrs.fr/wws/info/aria-discuss
If you have any more questions please get in touch.