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Re: [modeller_usage] Imposing dihedral restraints



Vivek Sharma wrote:
I am having some troubles in putting dihedral restraints in the system I am modelling.

So for e.g. I put a dihedral restraint (say phi for e.g.) for a residue like this:

SET ATOM_IDS = 'C:317' 'N:318' 'CA:318' 'C:318'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 11 4 2 0 -1 0.261

This should be fine, provided that you really want the mean to be -1 radians, and that this is within the 'special_restraints' routine or similar: http://salilab.org/modeller/manual/node32.html

Now when I run modeller with such restraints, in the finally obtained models, I dont see these exact values of restraints, which we mentioned explicitly, taken in by the model. Why this is so? The values of these mentioned dihedral restraints in
the modelled models are far from the prescribed values.

You should check the log file to make sure the restraint is actually there, and the end of the .rsr file.

Now as I said above that I am giving 15deg as std. deviation,but when I use smaller values like 5deg or so, the program is getting failed, it seems that it is getting difficult for it to optimise the system, with smaller values of std. deviation.

Last but not least, what I tried or trying is that creating the gaps in this section of 5 residues, where I am imposing backbone dihedrals, so that MODELLER doesnt find any equivalent residues in that position in templates and probably reduces the number of restraints, and in that case I may be able to impose my restraints well enough for these five residues, but still results doesnt seems to go hand in hand. Any comments in this concern also will be helpful.

If you actually are applying the restraint, it is probably being violated because it clashes with an existing restraint. Modeller will apply dihedral restraints to your system regardless of whether homology information is available (if unaligned, it will just use CHARMM parameters). Therefore you should remove the existing restraints first: see http://salilab.org/modeller/FAQ.html#4 and the 'cispeptide' script in modlib/modeller/scripts/cispeptide.py (or the TOP equivalent in bin/__cispeptide.top) for an example.

	Ben Webb, Modeller Caretaker
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