Hello Miha,
you have to include a user distance-restraint, the concerning chapter in the manual about these restraints and the parameters used is named "2.5 Calculation of spatial restraints".
There is also the FAQ at http://salilab.org/modeller/FAQ.html, open it and look for "I want to add my own restraints".
This is an example (to be inserted in your .top file):
... [rest of your .top-file...] CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'CA:25' 'CA:187' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 1.0 SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE
I hope this helps you getting started. Best wishes and happy modelling,
Thorsten Schweikardt Molecular Biophysics Mainz, Germany
> > -----Ursprüngliche Nachricht----- > > Von: Miha Pavsic [mailto:miha.pavsic@ijs.si] > > Gesendet: Mittwoch, 3. Dezember 2003 10:54 > > An: modeller_usage@salilab.org > > Betreff: [modeller_usage] Upper limit distance restraint > > > > > > Hello Modeller users, > > > > I am looking for a way to specify upper limit distance restraint > > between CA atoms of two residues (eg., max 10 A between CA:25 and > > CA:187). Can someone please give me an example of doing this? > > > > Regards, > > Miha Pavsic > > >