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donaldlab / OSPREY3

Open Source Protein REdesign for You v3
GNU General Public License v2.0
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work with unusall groups in OSPREY, a complicated issue! #170

Open biotech70 opened 3 years ago

biotech70 commented 3 years ago

Hi. I want to work with an 8 aminoacids peptide contain Amine and Acetyl group at C and N-terminal, respectively. Before anything, I create amine and acetyl parameters by antechamber and add obtained parameters to all_nuc_94_and_gr.in, but yet OSPREY does not know these groups, how can I bypass this problem?

cuchaz commented 3 years ago

Honestly, I don't know how to prep new molecules for Osprey. I was hoping someone else would answer this one. We're working on a new easier system for doing exactly that, but it's not released yet. I don't really know how to get the old system working. There doesn't seem to be any recent documentation for it that I know of.

All I know is the old system is template-based, and the API for importing your molecule templates has an example here: https://github.com/donaldlab/OSPREY3/blob/main/examples/python.GMEC/templateLibrary.py

But I have no idea how one can create those templates. There is an automated tool that tries to do this that's maintained by a group outside the lab. I have no idea if it still works or not, but you could try that and see if it works for you? http://ospreyprep.com/

Otherwise, I think those templates can be created by AmberTools? Somehow? Or maybe even manually.

Hope that helps.

biotech70 commented 3 years ago

Thanks, dear Jeffrey, but OSPREY Structure Preparation Tool (http://ospreyprep.com/) has not worked. Ivelin Georgiev in OSPREY user manual (v1.0) in adding force fi eld parameters section depict this topic but this does not work with me.

biotech70 commented 3 years ago

Dr. Shahriar Arab Group at Tarbiat Modares University created a server (http://bioinf.modares.ac.ir/software/osprey) to prepare OSPREY input files and execute OSPREY (findGMEC algorithm only), but this server is also limited to native residues.

cuchaz commented 3 years ago

Ivelin Georgiev in OSPREY user manual (v1.0) in adding force field parameters section depict this topic but this does not work with me.

I think that documentation was written over 10 years ago now? It is very much out of date.

Dr. Shahriar Arab Group at Tarbiat Modares University created a server

Wow, cool. I didn't know about that.