Dear Benn,
I am having some troubles in putting dihedral restraints in the system I am modelling.
Firstly, I should say I want to put backbone angles (phi/psi) into a stretch of 5 amino acid residues. I mention the values
(these values are from database, in fact are right and do exist in one protein) with the std. deviation value ~ 15deg. And, I am using Modeller 7v7, sorry I am slow in updating myself ;).
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
So now you can see here;
Form is 3 Modality is 1 Feature is 3 (dihedral angle) group is 11 (Mainchain phi dihedral restraints) Numb_atoms = 4 Numb_parameters = 2 0 Value of angle in radians Std. deviation in radians.
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.
Secondly, though I dont see any violation also in concern to these values, i.e. if I have understood correctly, then
violation will be reported in the log file if (optimized value - value mentioned by used)/(std. deviation) > 4.5
(approximately something like that). So this makes clear that why violation is not reported, because our values (diff/std. devn) are less than
4.5. But the question is, that when I give value of 15 degree as std. deviation (which I have to, I will come to this point
later!) , then difference between optimsed value and mentioned value ~ 60 degrees, and that is very much. So again what I say
is that I want to put certain values of dihedrals (backbone angles in fact) in the model, but values obtained for these
angles in optimised models are far from the values mentioned in by me (because range of difference is ~60 degrees), though there are no violations reported, probably because of the above mentioned reason. PLease tell me what to do in this concern.
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. Also, please tell me how to solve this problem.
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.
Details: there are two templates, MD_LEVEL is refine_3, our own alignment and paramters are used. So overall these are the problems I am at the moment facing, so any comments/details, will be very helpful.
PS: The subject is different from 'Problem', :).
Thanks in advance,
br,
Vivek Sharma University of Helsinki.