March 2004 - modeller_usage

Re: modeller_usage Digest, Vol 3, Issue 36
by Azat Badretdinov 31 Mar '04

31 Mar '04

> Message: 4 > Date: Tue, 30 Mar 2004 16:55:59 -0500 > From: "Clemens Steegborn" <cls2001(a)med.cornell.edu> > Subject: [modeller_usage] problem reading alignment file > To: modeller_usage(a)salilab.org > Message-ID: <5.2.0.9.2.20040330164627.00b485d0(a)pop.med.cornell.edu> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > > 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! > Hi, Clemens, Weird. It is not clear why would you have to modify your libs.lib file, since normally it contains the setting for RESTYP_LIB? Do you have your own customized restyp.lib at a different location? I assume your *LIB settings in libs.lib are more or less similar (like in the default setting). If that is the case and if RESTYP_LIB setting would be incorrect, then other library settings would cause problems as well. I wonder if you can send your input files (.pdb, .ali, libs.lib and restyp.lib). Azat A.Ya.Badretdinov, PhD, Sr. Scientist x5728 http://intranet.accelrys.com/~azat > Clemens > > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 3, Issue 36 > *********************************************

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Re: [modeller_usage] problem reading alignment file
by Eric Feyfant 31 Mar '04

31 Mar '04

Hi Clemens; I suggest you to extract the sequence using modeller : basically: Read the pdb file set ADD_SEQUENCE on and write the alignment. And you will see what sequence modeller consider. As far as I know Modeller never had issues with gap and "/" which correspond to a TER in your pdb file. Eric >>> "Clemens Steegborn" <cls2001(a)med.cornell.edu> 3/30/2004 4:55:59 PM >>> 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 _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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RE: [modeller_usage] problem reading alignment file
by Schweikardt, Thorsten 31 Mar '04

31 Mar '04

Hi Clemens, the error you describe usually appears when your pdb- file has some missing aminoacids in respect to the sequence you use in the alignment-file. Modeller states that your pdb contains 392 residues, but your alignment contains 433. You can use DeepView to open your template and save its aminoacid-sequence (File-Save-Save Sequence as FASTA). Compare it to the sequence in your alignment file, they should be identical. If not, correct the align- ment. Hope this helps. Concerning the '/' and '-', I have no problems using them on the linux-version. Best wishes, Thorsten Schweikardt Molecular Biophysics University Mainz, Germany > I'm using the WINDOWS version of MODELLER6v2 > > I get the following error when reading the template and > alignment files: > >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)! >

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Count problem
by hemant kushwaha 30 Mar '04

30 Mar '04

Dear sir, I am facing a problem in getting my model of an allosteric enzyme and the prblem is with the count in the pdbfile and the alignment file the top file i am using is as follows: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'template.ali' # alignment filename SET KNOWNS = '1BDG' '1DGK' '1CZA' 1BG3' '1HKC' ' # codes of the templates SET SEQUENCE = '1Str' # code of the target SET ATOM_FILES_DIRECTORY = '/disk1/project/ratnesh/pdbfiles' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) SET HETATM_IO = on # include heteroatom in the model #SET WATER_IO = on CALL ROUTINE = 'model' # do homology modelling and the error i am getting in logfile is as follows: Read the alignment from file : templatefile.ali Total number of alignment positions: 953 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1HKB 905 3 1HKB undefined 2 1DGK 903 3 1DGK undefined 3 1CZA 903 3 1CZA undefined 4 1BG3 893 3 1BG3 undefined 5 1HKC 901 3 1HKC undefined 6 1Str 493 1 1Str Candida albicans TOP_________> 122 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKB.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1DGK.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 902 33 GLYP 113 ADP RTppp## rdabrk__288W> Protein not accepted: 2 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1CZA.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 3 903 33 GLYP 113 ADP Tpppp# rdabrk__288W> Protein not accepted: 3 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1BG3.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKC.pdb fndatmi_285W> Number of residues <> number of atoms; atom code: 905 901 CA check_a_337E> Structure not read in: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 20689357 20204.449 19.731 Starting time : 2004/03/29 17:26:50.612 Closing time : 2004/03/29 17:27:04.831 Total CPU time [seconds] : 0.00 Can u help in sorting out what is this error and how it can be solved warm regards hemant __________________________________ Do you Yahoo!? Yahoo! Finance Tax Center - File online. File on time. http://taxes.yahoo.com/filing.html

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problem reading alignment file
by Clemens Steegborn 30 Mar '04

30 Mar '04

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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Re: [modeller_usage] OBJECTIVE FUNCTION
by Matthias 30 Mar '04

30 Mar '04

Thanks a lot, i appreciated your help..

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Adding ligand in protein will solve sidechain confromatin problem?
by Nataraj Balkrishnan 30 Mar '04

30 Mar '04

Dear Modeller, I modelled a protein from low identies template,and more I am having the idea of location of active site for my modelled protien for particular ligands. Since I know the active site of the model, I want to construct the sidechain of aminoacids involved in that active site,by adding ligand in that particular location.(Since I belive that the configuration of sidechain in the state of interaction with ligand would be the actual conformation of the sidechains of active site). Now my questions are 1)Wheather my this idea is theoreticaly correct ? 2)if the answer for my question 1 is correct, what is the way or routine which I can use it for adding my ligand(small molecule,eg.,DDT) to my model? Kindly help me... Thank you in advance. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Can any get Z-score for my target sequence in PROSAII?
by Nataraj Balkrishnan 30 Mar '04

30 Mar '04

Dear Modeller, Sorry I don't know ,wheater It is ethical to ask as such help from your end. But I am helpless. I have modelled a protein in modeller from a low identiy template with respect to my target. I checked my internal verification of my model and external too ,such as PROCHEK ,whatchek etc., But PROSAII is one test that I have not attempted since I don't have that software. If any volunteers out there having PROSAII software, may help me to predict data (Z score or more) for my target protein. If any body willing please mail me up and send my coordinate to you. With regards, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Re: [modeller_usage] Adding ligand in protein will solve sidechainconfromatin problem?
by Eric Feyfant 29 Mar '04

29 Mar '04

Dear Nataraj; 1/ Theoretically, yes it seems valid but you will be confronted to several issues. 2 main ones could be: a/ You have to see if the active site is more conserved that the overall protein, don't expect to bind correctly a ligand in a pocket that share a low identity with your template (it also depends on your definition of low identity!). For example, in a case of Kinase, it is common to have low identity between the kinase (overall of 30-40%) but the ATP binding site, which is very often targeted in drug design, share a much higher identity (70 to 80%). b/ If your active site identity is not that an issue, you may need rearrangement of the side chain in order to bind correctly the ligand. But Modeller derived homology restraint from the template which doesn't have the ligand (I presume), therefore these restraints may become a problem for your optimization, especially side chain - side chain restraints. In that case I will suggest you 2 approaches: - you can delete the side chain - side chain restraints for the active site. - Build you model without the ligand and dock it after using a docking software. Now if you template as the same ligand bound into it and you have just some mutation in your active site therefor: Yes you can use your idea. And to add a small ligand check the FAQs on the manual, you will find some answers. Good luck! Eric ------------------------------------ Eric Feyfant, Ph.D. Senior research Scientist Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant(a)wyeth.com >>> Nataraj Balkrishnan <natarajmtech(a)yahoo.co.uk> 3/29/2004 1:11:10 PM >>> Dear Modeller, I modelled a protein from low identies template,and more I am having the idea of location of active site for my modelled protien for particular ligands. Since I know the active site of the model, I want to construct the sidechain of aminoacids involved in that active site,by adding ligand in that particular location.(Since I belive that the configuration of sidechain in the state of interaction with ligand would be the actual conformation of the sidechains of active site). Now my questions are 1)Wheather my this idea is theoreticaly correct ? 2)if the answer for my question 1 is correct, what is the way or routine which I can use it for adding my ligand(small molecule,eg.,DDT) to my model? Kindly help me... Thank you in advance. Yours truly, B.Nataraj Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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The selection of models
by Binbin Liu 29 Mar '04

29 Mar '04

Dear Modellers, 100 models were generated based on one template. Their atomic RMSDs all are less than 0.4 Angstroms. Does any body know any other way I can find a representative model from the 100 models. Many thanks. Binbin

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