- modeller_usage - salilab.org

special restrains for aromatic packing interactions
by Thomas Evangelidis 03 Mar '10

03 Mar '10

Dear Modellers, I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic: http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_… I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here: http://salilab.org/modeller/manual/node196.html Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome. thanks, Tom

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ligand desgin
by Knut J Bjuland 02 Mar '10

02 Mar '10

I am using a model designed with modeller to do docking. Howevere there is problem with ligand design. The ligand is gogin to be 4 peptides long and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other postion should be any amino acid. How can I design a peptide with 20**3 different amino acids. Or can you point me to a software that do ligand desing or a good database. Knut J _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

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Re: [modeller_usage] Improving the structure
by bharat lal 01 Mar '10

01 Mar '10

Hi all, I have modelled a structure with a template having 24% identity as per the pdb blast result .. and my template had formylated glycine which I also wanted in my model so i modelled the structure using model-ligand.py script.. The verify 3D score of that model is coming as 60% only .. can anybody tell me how can i improve the score .. I modeled some 50 structures and then for the best one I went for loop modeling and then loop refining using modeler only but I am not able to increase the score .. can anybody tell how can i improve the scores and structure too.. thanks Bharat Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/

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cofactor symbols II
by Joel Tyndall 01 Mar '10

01 Mar '10

Found it... \Modeller9v7\modlib\restyp.lib Contains all of them, heme, adp, atp...and heaps more _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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cofactor symbols
by Joel Tyndall 01 Mar '10

01 Mar '10

Hi folks, Can anyone tell me where to find the list of cofactor symbols that modeller accepts, e.g. Heme, ATP, ADP etc. Ta J _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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special restrains for aromatic packing interactions
by Thomas Evangelidis 26 Feb '10

26 Feb '10

Dear Modellers, I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic: http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_… I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here: http://salilab.org/modeller/manual/node196.html Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome. thanks, Tom

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Phosphorylated Residues - Phospotyrosine (PTR)
by Jan H. Löhr 24 Feb '10

24 Feb '10

Hello everybody, my question has already been posted a couple of times - however these posts date back a couple of years. That is why I hope to find new answers to this topic. Modeller (9v7) does not recognize phosphotyrosine residues (Phosporylated tyrosines, PTR). There are three options to deal with such undefined residues: 1. Use Tyrosine instead (and optionally after modelling: replace with phosphotyrosine und minimize) This might be a good choice, if the residues were in areas far away from the region under investigation 2. Use Block Residue (rigid body) - not the most accurate way, but a good workaround (http://salilab.org/modeller/9v7/manual/node95.html) 3. Define the unknown residue according to the manual/FAQ (http://salilab.org/modeller/FAQ.html#8) I would prefer the third option and define them myself, but as the manual states, this is a "painful" process. I wonder if anyone has generated the needed files/entries for the modeler libraries. There is a page in the Modeller Wiki that allows upload of these customized files. It is empty however. Since I currently do not have access to QUANTA or CHARMM, I cannot generate the files myself. I also wonder why the library file for residues in modeller 9v7 still dates back to 1993? I hope someone can help. Thank you in advance, Cheers Jan H. Loehr University of Hamburg, Germany

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Optimization
by abdullah ahmed 24 Feb '10

24 Feb '10

Hello, I just wanted to know if it was possible to conduct optimization in such a way that Hydrogen atoms are present in the optimized structure/protein? Thanks in advance, Abdullah _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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questions concerning hydrogen in optimization
by abdullah ahmed 24 Feb '10

24 Feb '10

Dear Laurent, I have a question regarding optimization using "cg.optimize". The optimized structures/proteins produced after using this function are always without hydrogens. So does this mean that: The optimization procedure removes hydrogens and does not use them during the optimization steps?If the above is true, is there a way to conduct optimization with hydrogens included? Thanks in advance, Abdullah _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Error when using flex-em
by Saskia Bakker 23 Feb '10

23 Feb '10

Dear Modeller support, When trying to fit the crystal structure in an EM map using mod9v7 and the flex-em script (unmodified apart from filenames) I get the following error message: bash $> /usr/bin/python ../../scripts/flex-em.py > flex.log File "/fbs/emdisk3/emsoftware/LINUX/modeller9v7/modlib/modeller/optimizers/molecular_dynamics.py", line 50, in optimize ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars) OverflowError: check_inf__E> Atom 1 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. It happens when running in CG mode and MD mode. The map is 140x140x140 pixels, which is already 1/8 of the complete map (using the complete map gives the exact same error). There are 893 residues (6 rigid body domains) in the model I am trying to fit. It gives the same error with poly-Ala. Are these files too large? The coordinates of the pdb files that are output after the first iteration look sensible and fit well in the map (but not quite well enough). I would be very grateful for any suggestions to help solve this problem. Many thanks, Saskia

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