Re: [gmx-users] Noe distance restraints

I surely searched for answers looking through gromacs, charmm documentation, mailing list, web, literature, etc. before posting my question. I know that it sounds inappropriate because it isn't a technical question, nevertheless I still wasn't able to solve the apparent contradiction between NMR da

Re: [gmx-users] Noe distance restraints

Chiara Parravicini wrote: Do you refer to pages 58-61 or 148-149 of the manual, about distance restraints and NMR refinement? Yes. Having read them, and having worked out how to implement them in the context of the tables in section 5.6 4 is prerequisite to you solving your problem :-) "How

Re: [gmx-users] Noe distance restraints

Do you refer to pages 58-61 or 148-149 of the manual, about distance restraints and NMR refinement? In that case is still not clear to me if the authors in the cited paper use simple distance restraints or apply NMR-derived data, given that the model presented is based on a X-Ray structure. So,

Re: [gmx-users] Noe distance restraints

> Dear Gromacs users, > > I'd like to perform a simulation following the protocol applied in the > Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor. > Ligand > docking and identification of a putative binding site of the distal hexose > moiety.* *Bioorg. Med Chem Lett.* 2007;17

[gmx-users] Noe distance restraints

Dear Gromacs users, I'd like to perform a simulation following the protocol applied in the Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ).

[gmx-users] NOE distance restraints

Dear Gromacs users, I intend to perform a MD simulation of a GPCR model applying distant restraints to the backbone of alpha helices, something like NOE distance restraints. I guess that gromacs can't do it directly but if I've well understand I can manually provide classical distance restraints i