May 2002 - modeller_usage

Topology and parameter files for sugar residues in glycoproteins
by Andersen, Kim Vilbour (KVA) 17 May '02

17 May '02

Hi I'm trying to model a glycoprotein with Modeller and would like to include the glyco-part in the modelling. I'm fighting with the creation of topology files (and parameter files) creating the topology of the different involved sugar residues as well as patch residues to create the relevant bonds. Has anybody out there done this already and are willing to share? I'm mainly interested in N-acetylglucosamine, N-acetylgalactosamine, Mannose, Galactose and Sialic acid as well as the relevant patchings. Any input will be appreciated, thanks Kim ------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Principal Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark ------------------------------------------------------------------------

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None
by Mensur Dlakic 15 May '02

15 May '02

Hello, There is a bug in iris4d v6.2 when fitting models to the original structure using SET FINAL_MALIGN3D = 1. To be more precise, original models are reoriented properly, but loop-optimized models are not. It looks something like this: HETATM 323 PCA 6.BL0 58.234 76.175 42.150 1.00110.73 1SG 324 HETATM 324 PCA 6.BL0 58.860 77.458 42.113 1.00110.73 1SG 325 HETATM 325 PCA 6.BL0 59.060 78.039 43.525 1.00110.73 1SG 326 HETATM 326 PCA 6.BL0 57.719 78.207 44.162 1.00110.73 1SG 327 HETATM 327 PCA 6.BL0 57.087 77.136 44.752 1.00110.73 1SG 328 HETATM 328 PCA 6.BL0 57.092 79.431 44.186 1.00110.73 1SG 329 HETATM 329 PCA 6.BL0 55.854 77.282 45.346 1.00110.73 1SG 330 HETATM 330 PCA 6.BL0 55.861 79.586 44.775 1.00110.73 1SG 331 HETATM 331 PCA 6.BL0 55.238 78.509 45.357 1.00110.73 1SG 332 HETATM 332 PCA 6.BL0 60.210 77.157 41.537 1.00110.73 1SG 333 HETATM 333 PCA 6.BL0 60.927 76.297 42.048 1.00110.73 1SG 334 while the original file before MALIGN looks like this: ATOM 323 N PHE 42 58.234 76.175 42.150 1.00110.73 1SG 324 ATOM 324 CA PHE 42 58.860 77.458 42.113 1.00110.73 1SG 325 ATOM 325 CB PHE 42 59.060 78.039 43.525 1.00110.73 1SG 326 ATOM 326 CG PHE 42 57.719 78.207 44.162 1.00110.73 1SG 327 ATOM 327 CD1 PHE 42 57.087 77.136 44.752 1.00110.73 1SG 328 ATOM 328 CD2 PHE 42 57.092 79.431 44.186 1.00110.73 1SG 329 ATOM 329 CE1 PHE 42 55.854 77.282 45.346 1.00110.73 1SG 330 ATOM 330 CE2 PHE 42 55.861 79.586 44.775 1.00110.73 1SG 331 ATOM 331 CZ PHE 42 55.238 78.509 45.357 1.00110.73 1SG 332 ATOM 332 C PHE 42 60.210 77.157 41.537 1.00110.73 1SG 333 ATOM 333 O PHE 42 60.927 76.297 42.048 1.00110.73 1SG 334 If this is not informative enough, I can send whole files as attachments and also my .TOP scripts, though nothing seems to be wrong with them and everything else got executed fine. Mensur =========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur(a)umich.edu | ===========================================================================

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modeller4
by sasson iris 13 May '02

13 May '02

Hi I want to use modeller to expand CA models to full atom model. When i give modeller an alignment of the query with a sequence from a pdbfile it changes the position of the CAs, that is , my original model changes. Can i give modeller a parameter that sets restrictions regarding where the atoms around the backbone are positioned ? Can i set this restraint to some interval ? Thanks alot !!!! Iris. I

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Re: Modeller 4
by Dinesh Soares 13 May '02

13 May '02

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Modeller 4
by Dinesh Soares 13 May '02

13 May '02

Hi, I am currently using Modeller 4 to try and model a protein of interest. I was able to model this protein "DAF_2" using a single template "MCP_1" while providing the alignment directly for modelling. However, when I introduce a second template "VCP_1" in the direct alignment, I get the following message (several thousand lines of it!) before the program exits: chkder___W> DVZ(i) out of bounds: 503 503nan chkder___W> DVX(i) out of bounds: 504 504 0.7392E+14 chkder___W> DVY(i) out of bounds: 504 504 -0.5166E+13 chkder___W> DVZ(i) out of bounds: 504 504 0.3008E+14 chkder___W> DVX(i) out of bounds: 505 505nan chkder___W> DVY(i) out of bounds: 505 505nan chkder___W> DVZ(i) out of bounds: 505 505nan chkder___W> DVX(i) out of bounds: 506 506nan chkder___W> DVY(i) out of bounds: 506 506nan chkder___W> DVZ(i) out of bounds: 506 506nan chkder___W> DVX(i) out of bounds: 507 507nan chkder___W> DVY(i) out of bounds: 507 507nan chkder___W> DVZ(i) out of bounds: 507 507nan getcells__E> internal error; nx,ny,nz,cell,icel,maxcell: ************************ 4.000******** 208000 MY TOP FILE: model-double.top INCLUDE #include modeller routines SET ALNFILE = 'DAF_2-MCP_1-VCP_3.ali' #alignment file SET KNOWNS = 'MCP_1' 'VCP_3' #known templates SET SEQUENCE = 'DAF_2' #target sequence file SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 #generate 5 models CALL ROUTINE = 'model' #get models MY ALIGNMENT FILE: DAF_2-MCP_1-VCP_3.ali >P1;MCP_1 structureX:MCP_1:1:A:61:A:::: -CEEPP-TFEAMELIGKPKP-YYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACY* >P1;VCP_3 structureX:VCP_3:128:A:183:A:::: KCQSPPSISNGRHNG-Y-ED-FYTDGSVVTYSCNSGYSLI-GNSGVL-CSGG-EWSDP--PTCQ* >P1;DAF_2 sequence:DAF_2 SCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWS-TAVEFCK* Please advise!! If you require the PDB files, please let me know. Thanks in advance, Dinesh _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx

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Comparing energy terms
by Dan Thomas Major 12 May '02

12 May '02

I have a few question concerning the energy terms computed by MODELLER: 1) Can the energy of a model computed with loop-modeling be compared to the energy of a model computed without? 2) Can the energy of a model with an additional constraint added (like a specific distance constraint) be compared to the energy of a model without that specific constraint? 3) What kind of energy difference can be considered to reflect a significant difference in the quality of models? Sincerely, Dan Thomas Major -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Phone: 972-3-5317785 Fax: 972-3-5348730

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Re: 6v2
by Bozidar Yerkovich 10 May '02

10 May '02

Hi, Although we were hoping to release 6v2 this week, we run into some problems with Mandrake executable and we are currently working on it. As soon as this problem is solved we will release MODELLER 6v2. Thanks for your patience, Bozidar On Fri, 10 May 2002, Valeria Costa wrote: > > Dear Bozidar Jerkovic, > > I would like to know if the MODELLER 6v2 is know > available and if not when you think it would be. > > Thank you, > Valeria > > > On Thu, 21 Mar 2002, Bozidar Jerkovic wrote: > > > > > Hi, > > > > Please go to the MODELLER web site at: > > http://salilab.org/modeller > > ...and download MODELLER 6v1 > > > > Also we will have MODELLER 6v2 in a few weeks. > > > > Happy modeling, > > Bozidar > > > > > > > > On 21/3/02 3:40 AM, "Valeria Costa" <costa(a)sissa.it> wrote: > > > > > > > > Hi, > > > > > > I didn't know there were two 6 versions! > > > I have "modeller6a", as I read the preliminary release of version 6, > > > of December 13, 2000. > > > > > > Thanks a lot for help, > > > > > > Valeria > > > > > > > > >

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Modeller in queue
by Dan Thomas Major 08 May '02

08 May '02

Hi, I was wondering if anyone has experience using Modeller through a queue. I'm trying to run Modeller6v1 using the NQS queueing system on an Origin2000 machine (SGI). I get the following error: sys-2 : UNRECOVERABLE error on system request No such file or directory Encountered during an OPEN of unit 11 Fortran unit 11 is not connected IOT Trap /usr/spool/nqe/spool/scripts/++1qK++++27+++[6]: 399544 Abort(coredump) I manage to run Modeller interactively on the same machine. Attached is the NQS script used: #QSUB -s /bin/sh #QSUB -l mpp_p=1 #QSUB -lt 172800 #QSUB -lm 100MB /usr/home/chem/majord/bin/modeller/modeller6v1/bin/mod6v1_iris4d refine-loops3.top > refine-loops3.log Sincerely, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Phone: 972-3-5317785 Fax: 972-3-5348730

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modeller
by Andras Fiser 07 May '02

07 May '02

Hi modeller is not running parallel. The only way to take advantage of multiple processors is to run parallel modeller jobs. It is useful if you need to calculate many models for a protein, let say, with various alignments, or with various templates. Running multiple modeller jobs is particularly useful if you do loop modeling, since you need to generate numerous models before you select the one with the lowest energy. Pay attention that in this case you need to change the RAND_SEED, which is responsible for random number generation, otherwise you get identical models. best wishes, Andras ------ Forwarded Message From: Douglas Kojetin <djkojeti(a)unity.ncsu.edu> Date: Sun, 05 May 2002 23:13:47 -0400 To: modeller_usage(a)salilab.org Subject: using modeller w/ multiple CPUs Hi- Does anyone know if MODELLER can take advantage of a multiple CPU system? If so, how to set it up? Many thanks, Doug Kojetin -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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LJ potentials
by Evers Andreas 05 May '02

05 May '02

Hello! I would like to introduce Lennard-Jones potentials between two different sets of atoms ((1) all HETATMS and (2) all protein atoms in a 7 A environment shell around the HETATMs). Which commands do I have to include into the top file to do this? Thank you in advance for your answer, Andreas -- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers(a)mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################

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