- modeller_usage - salilab.org

How to introduce a covalent bond in a model?
by DimitryASuplatov 19 Sep '08

19 Sep '08

Hello, I want to link N-end of the chain alpha with C-end of the chain beta in my peptide. Terminal acids are quite near to each other (4 A), thus it is possible. I have made up some workarounds like switching the chains in pdb and seq files before making the alignment for modeller etc.; I dont like it though. I suggest that there should be some universal function built-in modeller for this kind of purpose. Do you know how to manage this? Thank you. I appreciate your help. SDA

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CHARMM atom type is not recognized (not in RADII_LIB): 15.999
by Wang Yanli 09 Sep '08

09 Sep '08

Hi, Modeller When I add the ligand (Allosamidin) as new residue type. I use insightII to generate the rtf file, ad add information in *.lib files. But I still get bellow error. How can I do? Thanks! env.libs.topology.read(file='$(LIB)/top_heav.lib') File "/home/ylwang/bin/modeller9v4/modlib/modeller/topology.py", line 23, in read return self.append(file) File "/home/ylwang/bin/modeller9v4/modlib/modeller/topology.py", line 27, in append return _modeller.mod_topology_read(self._modpt, self.__libs.modpt, file) _modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): 15.999

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(My) problems with BLK
by Francesco Pietra 08 Sep '08

08 Sep '08

I posted to a wrong list of Modeller, so I got no answer. Here the latest from my efforts, trying with a single chain to simplify. My pdb file ends like: HETATM 3346 CLA BLK A 859 78.668 51.520 63.082 1.00 26.90 CLA END In the ali file, CLA is represented as a dot "." in both the structure and the sequence, without "/", i.e., CLA is in the same chain. Models are built as if they had good DOPE score, though the log file complains: iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: CLA --> CT2 This message is written only for the first such atom. Although I am unfamiliar with CHARMM (I use Amber), I understand that my setting of BLK is incorrect, CLA is represented by a wrong atom type (CT2 stands for some carbon?). I tried variants, vainly. I looked at toppar files on the web, being unable to find the ten-entries long range and 1-4 non-bonded soft sphere terms for CLA to introduce in my /modlib/modeller/radii.lib. Such parameterization is available for SOD (just to talk about a single-atom ion) both on the toppar files and in Modeller itself, just in the radii.lib and radii14.lib. What I am trying is to represent CLA (chloride ion) as accurately as possible, even if I am aware that the effective spatial situation depends on the environment (in particular the balance between ionic and covalent bonding) so that any set of literature data for CLA will hardly fit accurately my situation. Thanks francesco

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Re: [modeller_usage] how to fix some residues not lying in allowed regions of Ramachandran plot
by Frederico Arnoldi 07 Sep '08

07 Sep '08

Dear Ruchi, >On ssessing the stereochemical > quality of the model, I found that it had 28 outliers residues (phi, psi), that > were lying in disallowed regions of Ramachandran plot. Most of these residues > are functionally important and hence can not be ignored. Will it be fine to > select each of these residues and model them using loop modelling? I am not the greatest expert in the area, but, maybe, I could try to help you with somethings. You said you are working with a tetrameric model. It must be a very large model. The first point I think you should pay attention is: How large is it? Which percentage 28 residues represents? Of course 28 residues are not irrelevant, but I think you should put it on the right scale. In a 280 residues model it could mean your model is not good. On the hand, in a 2800 residues (we are talking about a tetrameric model), it just represent 1%. Any way, the suggestion you have already received in the first answer is one manner to correct "mismodelled" residues. But don't forget the begining, your template. Even, making more models. Another point is that residues in disallowed regions generally means mismodelled residues, but them can also be related with important functions and these "wrong" angles are indicative of functionally important positions (there are a few papers discussing it, but I am not really updated). Check the template. Do these residues have "allowed" angles? And in other homologous structures? I hope my email help more than confuse you. Good luck, Fred The _________________________________________________________________ Receba GRÁTIS as mensagens do Messenger no seu celular quando você estiver offline. Conheça o MSN Mobile! http://mobile.live.com/signup/signup2.aspx?lc=pt-br

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how to fix some residues not lying in allowed regions of Ramachandran plot
by rsachdeva＠imtech.res.in 03 Sep '08

03 Sep '08

Dear All, I built 200 tetrameric models of my protein using 2 templates. I selected best model as the one having the least DOPE score. On ssessing the stereochemical quality of the model, I found that it had 28 outliers residues (phi, psi), that were lying in disallowed regions of Ramachandran plot. Most of these residues are functionally important and hence can not be ignored. Will it be fine to select each of these residues and model them using loop modelling? Or can anyone please suggest me some other (better) way of fixing such bad residues? With Regards Ruchi

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objective function
by Amanda Moraes 03 Sep '08

03 Sep '08

Hello! I heard that the lowest the objective function, better the model. But I haven´t found anywhere what is exactly objetive function and how it works. For example: I did with modeller 500 models from 3 templates, 500 models from 2 templates and 500 from 1 template. Can I compare the values of objective function from the 3 works? Or is it proportional for the number of templates used? Thank you in advance, Amanda Maia Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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'import site' failed; use -v for traceback
by DimitryASuplatov 02 Sep '08

02 Sep '08

Hello, when I execute Modeller 9v4 script I get python warning 'import site' failed; use -v for traceback Everything seems to work just fine though this message is a kind of annoying. I`ve searched the list and tried to tweak PYTHONHOME/PATH vars but that did not help. Furthermore I have python 2.5 installed and modeller uses built-in 2.3. Considering that I have no intentions of using external python modules could this message cause me a problem with my work? Thank you for your help. SDA

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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 58
by salam pradeep 28 Aug '08

28 Aug '08

For modeling using multiple templates, I have used 5 , 6 , 7 & 8 templates. The greater the number of templates, the lower the energy based on DOPE & ANOLEA How much is the maximum number of templates we can used for multiple templates. Can we used upto 10 templates or more or is there a higher chance of error for using more than 8-10 templates. Regards Salam Pradeep Bioinformatics Center Biotechnology Divison North-East Institute of Science & Technology Jorhat, Assam, India

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protein-dna complex modeling
by prasun kumar 21 Aug '08

21 Aug '08

Dear users, I am trying to model a protein DNA complex.but nucleotides are not defined in the rtp file of modeller. I went through the FAQs of modeller,there I got some clue to make a top file for nucleotides.But I am unable to make charmm top file because I dont have charmm. so can you suggest any other method to make topology file. waiting for your suggestions. prasun kumar -- PRASUN (ASHOKA)

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Chaining models
by Stéphane Téletchéa 21 Aug '08

21 Aug '08

Dear colleagues, I'm using modeller to model in two or three steps my system. I'm first modelling conserved residues (10 models), and then use the best model (from modeller's objective function) to produce the loops. >From this first to the second step, i'm using a script, but i was figuring if there was a built-in function to do this automatically (so i could merge the two steps into one script). I would think of best_model.py or something like this, but i'm not sure if this exists (i think i saw something like this once but i've not been able to find it again). Thanks a lot for yours answers, Stéphane -- Stéphane Teletchéa, PhD. http://www.steletch.org

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