November 2009 - modeller_usage

HIS and HSE
by Francesco Musiani 15 Dec '09

15 Dec '09

Hello, I would like to calculate an all atoms (including hydrogens) model of a metallo protein containing zinc. In particular, I would like to bind Zn2+ ion to ND1 atom of an histidine residues. I try to replace the residue "H" with "6" in the alignment (I referred to restyp.lib library found in modlib directory) but I obtain the following error in the log file. getpdf__392E> Your library requires all bins zero; nbinx: 5 can you help me? regards, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it

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atom clashed
by leuven 10 Dec '09

10 Dec '09

Dear all: When I get the models from modeller, there are always some atom clash。How to solve this problem? Could modeller solve this by itself? I get models from "model-changeopt.py", and set a.md_level = refine.slow a.repeat_optimization = 50 Here is the results for the best model: Strongest energies for the vdWaals interactions _____________________________ _______________ 1 236 .GLU.N - 236 .GLU.CD 2.697 1.7143 2 318 .ASP.CG - 318 .ASP.C 2.844 1.7121 3 278 .ASP.CG - 278 .ASP.C 2.845 1.7029 4 99 .ASP.O - 101 .ASN.N 2.532 1.6450 5 143 .ARG.O - 161 .GLY.N 2.547 1.4700 6 250 .TYR.CG - 250 .TYR.C 2.885 1.3172 7 244 .ASP.O - 248 .ASP.N 2.563 1.3145 8 214 .ASP.CG - 214 .ASP.C 2.888 1.2951 9 411 .THR.O - 412 .LEU.C 2.710 1.2663 10 385 .ALA.O - 386 .ASP.C 2.713 1.2380 11 244 .ASP.N - 249 .ARG.O 2.578 1.1794 12 275 .SER.HA - 285 .ILE.O 2.185 1.1460 13 294 .ASP.O - 295 .GLY.C 2.725 1.1418 14 289 .TRP.CG - 289 .TRP.C 2.907 1.1394 15 276 .PHE.CG - 276 .PHE.C 2.914 1.0910 _____________________________________________________________________________ Strongest energies for the H-bonds interactions ____________________________________________ 1 344 .ASN.HD21- 344 .ASN.O 1.850 -1.5000 2 442 .ALA.O - 445 .SER.H 1.850 -1.5000 3 96 .GLY.O - 105 .VAL.H 1.850 -1.5000 4 397 .GLY.O - 399 .THR.H 1.850 -1.5000 5 230 .LEU.H - 235 .PHE.O 1.850 -1.5000 6 134 .ASP.OD2 - 164 .ARG.HH12 1.850 -1.5000 7 353 .ILE.O - 511 .ALA.H 1.850 -1.5000 8 398 .SER.HG - 398 .SER.O 1.849 -1.5000 9 106 .GLN.HE22- 142 .PHE.O 1.849 -1.5000 10 71 .PRO.O - 74 .LYS.H 1.849 -1.5000 11 206 .SER.HG - 208 .GLN.O 1.848 -1.4999 12 478 .ASP.O - 480 .SER.H 1.848 -1.4999 13 365 .VAL.O - 475 .SER.H 1.852 -1.4999 14 56 .LEU.O - 59 .TRP.HE1 1.848 -1.4999 15 177 .ASN.OD1 - 180 .LYS.H 1.852 -1.4999 _____________________________________________________________________________ Strongest energies for the Elect. interactions ____________________________________________ 1 31 .HIS.HE2 - 117 .PRO.O 1.872 -6.9175 2 50 .HIS.HE2 - 118 .TYR.O 1.940 -6.4947 3 406 .PRO.O - 513 .ASN.OD1 2.707 6.0365 4 348 .ASP.O - 513 .ASN.O 2.771 5.8644 5 294 .ASP.O - 295 .GLY.C 2.725 -5.8603 6 385 .ALA.O - 386 .ASP.C 2.713 -5.8427 7 340 .VAL.O - 524 .LEU.O 2.774 5.7495 8 411 .THR.O - 412 .LEU.C 2.710 -5.7430 9 326 .GLN.O - 488 .GLY.O 2.738 5.6908 10 9 .HIS.HE2 - 483 .GLU.OE2 1.871 -5.6896 11 134 .ASP.O - 135 .ILE.C 2.798 -5.6414 12 201 .ASP.O - 225 .VAL.O 2.878 5.5602 13 362 .GLN.OE1 - 530 .ASP.O 2.901 5.5484 14 386 .ASP.O - 387 .LEU.C 2.822 -5.5457 15 441 .ASP.CG - 441 .ASP.O 2.899 -5.4778 _____________________________________________________________________________ Non-bonded contributions _________________________ Normal pairs H-bonds : N.pairs= 14516 energy= -861. Elect. : N.pairs= 687078 energy= -0.402E+04 vdWaals : N.pairs= 699117 energy= -0.443E+04 1-4 pairs H-bonds : N.pairs= 5 energy= -0.137 Elect. : N.pairs= 21311 energy= 0.430E+04 vdWaals : N.pairs= 21306 energy= 288. Total H-bonds : N.pairs= 14521 energy= -861. Elect. : N.pairs= 708389 energy= 282. vdWaals : N.pairs= 720423 energy= -0.414E+04 Total non-bonded energy : -0.472E+04

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Modeling ligands in the binding site
by Qinghua Liao 10 Dec '09

10 Dec '09

Hi modeller users, Can modeller do ligand-steered modelling? And what is the difference between the ligand-steered method and the mothods from the on-line tutorial of Modeling ligands in the binding site? Are they the same method? Thanks very much! All the best, Qinghua fantasticqhl(a)yahoo.com

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how to enbale mutiple CPU for modeller?
by leuven 28 Nov '09

28 Nov '09

Dear all: I found that Modeller just use ony one CPU on my computer but the CPU is four-core. how to enbale mutiple CPU for modeller? Thank you

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how to assign different template for different regions?
by leuven 25 Nov '09

25 Nov '09

Dear Sir: I would like to build models assining different templates for different regions. For exmple: PDB-A for 1-150aa, PDB-B for 151-220aa and so on. How to achieve this? Because different template has different homolog with different regions. Thank you very much.

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Mutate and refine residue placement
by Steve Seibold 18 Nov '09

18 Nov '09

Hello Modeller. Having successfully install the newest version of Modeller on my new machine (I ran some test cases), I would like to attempt the construction of a mutant of my protein using the tutorial: http://salilab.org/modeller/wiki/Mutate%20model. However, my protein has metal and DNA with it and, so, I am not sure how Modeller will deal with this. Can you inform me? I am worried that Modeller will simple fail with the error that it can not recognize certain atoms. If it does, is there away I can get around this? Could I do only a local (around the mutated site) minimization only, ignoring the rest of the protein? I tried to investigate this in the archives but didn't find it. Sorry if this is a repeat. Thanks ,Steve

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Re: [modeller_usage] Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hello Yes. It seems to be working fine now. I just thought the error message I was getting ( "Could not find platform independent libraries" etc.) was DUE to the KEY ID problem. But they are evidently two separate issues and neither is a *Fatal* error. I am now attempting to run sample scripts to verify installation. Thanks, Steve _____ From: Forlemu, Neville [mailto:neville.forlemu@mssm.edu] Sent: Tuesday, November 17, 2009 1:33 PM To: Steve Seibold Subject: RE: [modeller_usage] Installation problem? Hi Steve, I guess it installed fine. Just locate the executable file and you are good to go -----Original Message----- From: modeller_usage-bounces(a)salilab.org on behalf of Steve Seibold Sent: Tue 11/17/2009 11:28 AM To: modeller_usage(a)salilab.org Subject: [modeller_usage] Installation problem? Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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modelling with ligands (FAD FMN and NADP)
by Yerko Escalona 17 Nov '09

17 Nov '09

Hi I have a problem when i model the structure of proteins with ligands (hetatm = NADP, FAD and FMN), because some residues have improper bond, like the Asparagine make bond between the N and C(gamma), or Phenyalanine with wrong position of aromatic carbon. I try resolve this with the optimization of models with VTFM and MD&SA but the error in the bonds of residues is the same. Also try without ligands and that's work. I think the problem is of the ligands that make incorrect restriction to the protein and make that errors. I hope that you can help me. Bye (My native language is the Spanish, so sorry for the mistakes)

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Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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rotation!!!
by Cool Hunk 13 Nov '09

13 Nov '09

Dear Ben n all, i have got an issue about the side chain of some of the aminoacids that are part of some beta-strands in my predicted model.. is there any way that i can rotate specific amino acids so that their side chains orientation can flip outward which is inward in my predicted model... or can i rotate the whole strand to fix that issue.. second question regarding some loops in my model is that one loop kind of intersect the other or you can say passes in between/ thru the other and that makes my model unreal.. can you tell me, how can i resolve this issue???? Also can you suggest some tools, web or any way to validate my structure and look for the bad contacts if any, so that i could use this model for futher work.... Thanking in advance... Muhammad

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