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Hello-- > As I want to use the pararestraints program for Xplor-NIH, I wonder which > topology file I should use for my protein, which is a protein plus a metal > ion (Co2-) linked by S-EDTA. The metal ion is chelated to S-EDTA, and S-EDTA > is covalently bonded to Cys by -S-S-. In this case, I don't know which > topology file and parameter file (besides protein-1.0.par & protein-1.0.top) You'll probably keep the EDTA-Co(II) group rigid, but have to come up with parameters for the -S-S- linker region yourself- you might try using http://davapc1.bioch.dundee.ac.uk/prodrg/ to help. You might create a new residue type with the Cys-S-EDTA moity, or create a patch which modifies an existing Cys. Please let us know if you need more guidance on this. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDCeYAPK2zrJwS/lYRAn1rAKCIKvUYX3n0o4bDEpwPG0fag1XE1ACfQp6j r6rifrnidhmxQ3dLmI5D68s= =3hlE -----END PGP SIGNATURE-----
