Hi Olga-- > > > Hello Charles, > > We are modelling a 2-domain construct, where the domains are joined via a > flexible polypeptide linker and also via a Cys-Cys bridge. We would like > to model it by leaving the domains rigid, and allowing the Cys-Cys and > linker to move. We are trying to use your algorithm, described in > J.Mag.Res.2001, 152, 282 concerning fixed constraints. Thus far we have > failed to achieve our goal: it seems that when we rigidify the domains the > Cys-Cys and linker also freeze. What is the right syntax for this? I look > forward to hearing from you and thank you in advance for the help. >
What you need to do is place the following bit of code in your script after you've read pdb, psf and parameters: dynamics internal ! initial rigid-body minimization reset group = (resid x1:x2) group = (resid y1:y2) auto torsion end where x1,x2 y1,y2 are the residue numbers deliminating the two rigid domains. Remove the auto torsion statement if you don't want torsion angle dynamics. Please let me know if this doesn't work. Charles -- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 FAX: (301) 402-2867
