May 2006 - modeller_usage

Imposing dihedral restraints
by Vivek Sharma 14 Jun '06

14 Jun '06

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.

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Averaged RMSD for 100 models
by Robert Selwyne 01 Jun '06

01 Jun '06

Dear Benn Good Day !!!!!!!!!!!!! I had run MODELLER to produced model 1-100.pdb (100 models) of same acid sequence but different energy values. Now, i want to calculate the RMSD values for the models. I know that SUPERPOSE will do for me. But i couldnot correlate and implement the results. Say in VMD 1.8.4 in the RMSD calculator option, if Average is selected, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure. By the same manner, my first model is model1.pdb and now is superpose my model2.pdb and calculate an averaged RMSD. And on the next step i have to superpose my model3.pdb to the averaged structure and calculate new averaged RMSD and so on. model1.pdb | superposition | model2.pdb | now two structures are merged/superposed | calculate the averaged RMSD for the merged/superposed structure | now superpose model3.pdb to the existing superposed structure (model1.pdb+model2.pdb) | now totally 3 structures are superposed | CALCULATE AVERAGED RMSD FOR PRESENT SUPERPOSED STRUCTURE (MODEL1+MODEL2+MODEL3) and so on Could you please help me in carrying out the problem. can you help me in knowing how the script file looks. WIth regards robert Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/

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What's the difference of "refinement level" in MD
by Yun He 28 May '06

28 May '06

As subject, how much difference does the FAST or SLOW refinement level effect the final models in MD? Does it really worth for a loooong computation to build a more accurate model?

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code
by N.Arun Prasanna 25 May '06

25 May '06

sir, I have seen the advanced tutorial. The example there gives how to code when user wants to define restraints. But how to code for the one where I want to use the default restraint in my template? Just I want it to extract the hetatm present in the template and model it. It will be of great use if u help me in this regard. Thank you. prasanna

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Model protein with ligand bound
by N.Arun Prasanna 23 May '06

23 May '06

Sir, Is there any option to model a protein bound to ligand? Say a template used is complexed with ADP.. Regards, prasanna

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code
by N.Arun Prasanna 23 May '06

23 May '06

Sir, It will be of great help if u can send me a general py code to model using a template (1YMF) with HETATM -ADP Regards, prasanna

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Model a Tetramer from a Dimer
by Yun He 22 May '06

22 May '06

Hi, everybody, I have read some interesting threads about how to build a multi-chain model, but these questions are usually focused on building from templates with the same number of chains. Here is my question, how could I build a tetramer from a dimer, if any chain of this tetramer is similar to the chain of that dimer. Jarod

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GA341/DOPE/MolPDF which one for model selection?
by Yun He 22 May '06

22 May '06

Hi, everybody, Currently, I am working on a model based on a very low sequence-identity template (about 13%). I use an alignment to produce 30 models, and then I sort these models by their molpdf or GA341 or DOPE. However, the sorts turn out very different results, some models with higher GA341 scores takes higher DOPE scores. I am confused, which one should I choose? Jarod

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About the Modeller output in PDB format
by Yun He 21 May '06

21 May '06

Hi, everybody. The structures produced by MODELLER are stored in PDB format, what does the value in last column stand for? In a normal PDB file, there is a temperature factor column, but in the modeller structure, it is not like a temperature factor, what is it? THX ..... Jarod

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absolute restraints
by Michael Grabe 17 May '06

17 May '06

Dear Modellers, I am having trouble with my absolute restraints I have a restraints file read in that looks like this: MODELLER5 VERSION: MODELLER FORMAT R 3 1 11 34 1 2 0 3520 -16.00 0.01 R 3 1 11 34 1 2 0 3546 -16.00 0.01 R 3 1 11 34 1 2 0 3575 -16.00 0.01 And in my TOP file I add the restraint as follows: SUBROUTINE ROUTINE = 'special_restraints' READ_RESTRAINTS FILE = 'restraints.rsr' SET ADD_RESTRAINTS = on RETURN END_SUBROUTINE But it doesn't do anything. I am pretty sure that I am calling on everything correctly, and I have seen this problem posted by others before. Any idea? Thanks Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 1550 4th Street GD482 San Francisco, CA 94143 Michael.Grabe(a)ucsf.edu tel: ++ 415.476.4021 http://profplum.ucsf.edu/~mgrabe/

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