- modeller_usage - salilab.org

Fwd: problem reading alignment file
by Clemens Steegborn 16 Apr '04

16 Apr '04

Hi everybody, thanks for all the suggestions how to solve my problem with reading an alignment file (see below). The solution was to remove all spaces from the alignment! Clemens >Date: Tue, 30 Mar 2004 16:55:59 -0500 >To: modeller_usage(a)salilab.org >From: Clemens Steegborn <cls2001(a)med.cornell.edu> >Subject: problem reading alignment file > > >Hi, > >I'm using the WINDOWS version of MODELLER6v2 > >I get the following error when reading the template and alignment files: > > > > >TOP_________> 121 107 CHECK_ALIGNMENT > > > >check_a_343_> >> BEGINNING OF COMMAND > >openf5__224_> Open 11 OLD SEQUENTIAL myt.atm > >rdabrk__290E> Number of residues in the alignment and pdb files are > different: 433 392 > > For alignment entry: 1 > >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > >the problem seems to be that MODELLER doesn't understand the gap residue >'-', as it also >doesn't understand '/' (using '/' gives an error stating it doesn't know >this residue)! > >I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib >file, but that didn't help. > >Any suggestions would be appreciated! > >Clemens

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PDB Database updates
by Nicole Scherer 15 Apr '04

15 Apr '04

How to update the files CHAINS_3.0_40_XN.cod and CHAINS_all.seq?

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(no subject)
by jeanney.f 14 Apr '04

14 Apr '04

hi, i have done some dimer with modeller but the problem is that i don't know how to conserve the chain ID my template have the chain 'A' and 'B' and the target have no chain id does it exists a command line? JEANNEY François Centre de Biophysique Moléculaire Numérique Faculté Universitaire des Sciences Agronomiques de Gembloux 2, Passage des Déportés 5030 Gembloux (Belgium) Tel +32 81 62 25 21 Fax +32 81 62 25 22

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problem with using chain identifiers ...
by gowthaman ramasamy 14 Apr '04

14 Apr '04

hello list, I tried so many times with all the combinations (listed bellow) to specify the residue identifiers in following top script. purpose of this script is to extract sequence from pdb files. following is base script which extracts all the chains from that pdb file. read_model FILE = '1PFZ', sequence_to_ali atom_files = '1PFZ', align_codes = 'gowtham' write_alignment file='outputmyseq.pir' I wanted to take out all residues of a particular chain say A. I used MODEL_SEGMENT = '79P:A' '329:A' and it works fine. But if I dont know start and end residue numbers of a particular chain, how should i extracts only its sequence. i tried the following and did not work: ' :A' ' :A' '.:A' '.:A' ':A' ':A' '@:A' '@:A' '@:A' '@:X' '@:A' '@:@' and many more ...... -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314

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Re: [modeller_usage] How to get various conformar for a modelled protein?
by Luis Rosales 14 Apr '04

14 Apr '04

Dear B.Nataraj, > For my modelled protein, I want to analyis various possible > conformare it can assume,In that connection I want to know what is the > command or in build routine to create all possible conformation for > my modelled protein ? Thank you in advance. To analyze possible conformers avalible to your model, you can run a molecular dynamics simulation with implicit or explicit solvent. On the latter case you first add a water shell to your model and minimize just the water shell, and after that you minimize the water-protein assambly. Finally you run a looooooooong dynamic, sample conformations at regular intervals of the simulation and voila!! You now have several conformers of your model!! You can do a search on NCBI Pubmed to get more info on this (software, parameters, etc). As always, what you do is defined by your needs and the computing resources available to you. I hope this helps, Kind regards, Luis.

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dynamic restraints
by Thomas Duncan 13 Apr '04

13 Apr '04

I'd like to confirm the default and options for dynamic restraints. I believe the default is set, under the OPTIMIZE command, as DYNAMIC_SPHERE = on (all others off) and that this means that only soft-sphere overlap restraints are generated. Are all the other DYNAMIC_ options available (LENNARD, COULOMB, MODELLER, ACCESS) and, specifically, what type of nonbonded restraints are included if DYNAMIC_MODELLER is turned on? Thanks, Tom Duncan

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How to get various conformar for a modelled protein?
by Nataraj Balkrishnan 13 Apr '04

13 Apr '04

Dear modellers, For my modelled protein, I want to analyis various possible conformare it can assume,In that connection I want to know what is the command or in build routine to create all possible conformation for my modelled protein ? Thank you in advance. yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Regarding adding ligands to protein...
by Nataraj Balkrishnan 12 Apr '04

12 Apr '04

Dear Modellers, I have to add or define a new ligand to use it for modelling purpose. In this regard I want to know.... 1)Which liberary I have to change in modlib folder? 2)How it should be changed(I need here some sample of small molecule that you have changed in that liberary)? 3)Wheather we need to know all physical and chemical proterties of the ligand(small molecule),I mean, any of those details need to be incorporated as data inside liberary used for modeller. And things will be more appreciated if you could send me your complete input files for model building based on my this particular interested topic. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Re: FW: FAQ
by phanivijayg＠hotmail.com 12 Apr '04

12 Apr '04

Dear Modellers I have problem in my alignment file. i want to build structure for antibody. which has matching with the corresponding chains in the template. My first chain has nearly 110 aa which match with the 220aa template chainA and again my second chain has hit with the chain B. after chain A there are 100aa gapped and again hit with ChainB, again after that gap of 100aa. The problem is in template the two chains have seperate numbering. i dont want to build the chains individually. how can I then set my alignment file? I'm attaching alignment file with this. I already mailed to this address Modeller_usage(a)guitar.rockefeller.edu. but it was bounced back. so i'm sending u. sorry for the inconvenience. Thank you. with regards Phani Vijay

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Regarding Optimization output ........
by Nataraj Balkrishnan 11 Apr '04

11 Apr '04

Dear modellers, I did optimization for my modelled protein using molecular dynamics "OPTIMIZATION_METHOD = 3". If I decrease the temperature from 300(modeller default value )to lower temperatue (eg., 200K,100K) the total energy of the optimized model decreases ,if I increase the temperature from 300 to higher temperature (eg., 400,500)the total energy of optimized model also increases. I do aware of that as the energy minimizes ,the model approaching its native nate or perfection. My question now is 1) wheather this behaviour happens with all protein (I mean increasing energy with initial temperature and vivevarsa)? 2) What are the useful conclution that I can derive out of this behaviour of my modeled protein ? Looking forward keenly to hear something from you. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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