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.
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
Hi Benn,
Replying late, but please see below;
On 5/30/06, Modeller Caretaker modeller-care@salilab.org wrote:
> 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
Yes I am using 'special_restraints'.
> > 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.
Yes the restraints explicitly mentioned by me are there in the log file as well as in 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.
Actually, here I didnt got the point completely. I did a little checking like this, please see:
Template sequence : FINR Target sequnece : FINR
PDB available for template. The target seq. has been modelled in various ways to check what kind of restraints are generated for a residue (N here, the third residue Asparagine), when there is a exact residue in the template at the equivalent position OR when there is a gap in the equivalent position OR when there is a different residue in the equivalent position. Now if we see below then the third residue has a different cases in the equivalent position in these three separate cases. I then checked restraint generated for each atom of the third residue i.e. N in target.
Cases: FINR FI-NR FINR- FINR FINR- -FINR
Results: The second case in which there is a gap in equivalent position in template i.e. for N, the restraints generate were least (for the atoms of this residue), clearly. And, the restraints are :
N stereo + phi-psi + omega + chi1 CA stereo + phi-psi + omega + chi1 + chi2 CB stereo + chi1 + chi2 CG stereo + chi1 + chi2 OD1 stereo + chi2 ND2 stereo C stereo + phi-psi + omega O stereo
I havent mentioned the restraints for the two other cases, but clearly the restraints (type and no.) were different from these. ""So I kind of consider it safe to create a gap at the position where I want to put my own restraints on, because in this case the MODELLER generate restraints are least"".
Now if you remember, then I had this problem that values which I was using for restraints was not imposed properly in the system modelled and you suggested that there might be some restraint clashes and if we see above case, in which there is gap and MODELLER generated restraints are least, we still have Phi-Psi binormal restraints. They probably might be clashing with the Phi-Psi values I am imposing (I am imposing Phi/psi dihedral angle restraints separately not the binormal ones), so I deleted them (Phi-psi binormal ones, which are generated by MODELLER and I checked log files and *.rsr that they are deleted) and generated the structure, but again no result, I still have restraint violations OR the values are very far from the values mentioned.
So I am not sure what I am missing or doing wrong, but it seems to me that probably some awkward values of dihedrals can not be modelled in MODELLER, though the values I am using to model are not awkward as such because they are derived from one protein (X-ray), I dont know the solution of this problem at the moment.
If you have any comments and they are very welcome. I am still trying few other options and checking, I will let you know whenever I have something in this concern. But any opinions will be great.
Have a nice day!
Vivek
> Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
-
Modeller Caretaker -
Vivek Sharma