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Hello Isabell-- You actually wrote to the list administrator email address. I'm replying to the full Xplor-NIH list. > > we are currently using XPLOR-NIH to determine NMR-constrained protein > structures. I have modified one such protein to incorporate two > fluroescent dye molecules (attached to a glutamine and cysteine side > chain) and performed FRET experiments. I am now attempting to > incorporate these modified amino acids in XPLOR. > > The Dundee PRODRG server (davapc1.bioch.dundee.ac.uk/prodrg) provided > me with paramter and topology file for the dye molecules attached to > their respective amino acid built using a molecular mechanics program > with ab initio minimization. Unfortunately, although I can generate a > .psf file with these modified residues, I am unable to produce an > extended protein structure, .pdb file. what exactly is the problem you are facing? > > The fluorescent dyes are based upon AlexaFluor 555 maleimide and > AlexaFluor 647 cadaverine (both with a rhodamine-like core) and > therefore contain fused aromatic ring systems. We suspect that some of > the errors might be due to lack of planarity terms in our topology and > parameter files. possible. Sometimes, you have to change dihedrals into impropers to get desired geometries. > > We would be grateful if you could provide us with any information on > how we might define these correctly and if you have any additional > information on topology files developed for fluorescent dyes or > modified amino acids this would be extremely useful for us. > > We have attached the topology and parameter file we are using. The > modified amino acids are labelled DRG and DRE, respectively. > One suggestion: use XPLOR atom naming for the backbone and non-modified portions of the sidechains. It may take a bit of fiddling, but it allows more use of built-in Xplor-NIH functionality. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJpxAAPK2zrJwS/lYRAhLEAJ9I/nTPBNPGXn1iw0R5LVJQSYf1xQCeJgKp TuJhVffiW/0XqA5zI8s0B9g= =JN1X -----END PGP SIGNATURE-----
