December 2002 - modeller_usage

assign force field
by Yang Xiaolin 25 Dec '02

25 Dec '02

Deal all, When I assigned force field to a protein 3D coordinate, I was told that "total formal charges does not equal total partial charge". I have added hydrogen to this structure. And If i change to another force field, the same thing happened. Who can tell me how I can resolve this problem. Thanks. Happy New Year to all! Xiaolin Yang

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error 648 with modeller
by Cédric Bauvois 17 Dec '02

17 Dec '02

Hi, I have a problem with Modeller program to make mutagenesis project by using triton. I always obtain the error message in the run_output file: Kind, OS, HostName, Kernel, Processor: 4, Linux pcb311 2.4.19-16mdk i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2002/12/17 11:07:34.945 getprog_531; ROUTINE redefined: loop getprog_531; ROUTINE redefined: loop_restraints getprog_531; ROUTINE redefined: optimize getprog_531; ROUTINE redefined: getnames-loop getprog_531; ROUTINE redefined: build_ini_loop getprog_531; ROUTINE redefined: select_loop_atoms rdpir___648E; Alignment sequence not found in PDB file: 1 . 2dhc.pdb recover____E; ERROR_STATUS = STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 12188765 11903.090 11.624 Starting time : 2002/12/17 11:07:34.945 Closing time : 2002/12/17 11:07:39.685 Total CPU time [seconds] : 3.96 STOP can you explain how to resolve these error? thanks a lot! Bauvois cedric

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floating invalid
by Marcos Bonfadini 16 Dec '02

16 Dec '02

Hi, modellers I've got this message: TOP_________> 197 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15156027 14800.808 14.454 make_re_417_> Restraint type to be calculated: distance forrtl: error (65): floating invalid Abort (core dumped) Can anyone tell me what went wrong? Thanks in advance Bonfá -- ////////////////////////////////////////////////// Marcos Bonfadini CBME-Centro de Bioteclogia Molecular e Estrutural Instituto de Física - USP / São Carlos Av.:Trabalhador Sãocarlense,400 - Centro C.P.369 - 13560-790 São Carlos - SP - Brazil Phone: ++55 16 273.9874, ++55 16 273.9868 FAX: ++55 16 273.9881 \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ Doações/Donations http://www.clickfome.com.br http://www.thehungersite.com http://www.doegratis.com.br

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leaving gaps in non aligned regions
by Gowthaman R 12 Dec '02

12 Dec '02

hello modellers, i am trying to model some proteins. but my protein has some region (internal) (15-20 amino acids) which does not have any corresponding region in the template sequence. i DO NOT want to model that region and in my final (3D) strucuture i want to have a gap in the corresponding internal region. other wise that region forms a loop or extended region ( makes the structre ugly ??). i wish to know how my alignement file should look like.... i tried following and did not solve the problem 1) putting " X " for the amino acids for which i dont want the 3D structure to be made 2) puting " - " for the same... waiting for ur reply gowthaman Phd Student ICGEB, India.

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# SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6
by Bozidar Yerkovich 11 Dec '02

11 Dec '02

On behalf of kinsellg(a)tcd.ie... Hi all, I've recently started using modeller and I've been able to generate models and loops, so far. I tried optimising my alignment and I've now hit this snag. I get this error when trying to generate loops. Also I havn't been able to get the command to optimise the loop envirionment to work yet. The top and log files are attached. # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 Any ideas?? I am very grateful for all your help, Gemma The error: TOP_________> 189 674 SET OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200, MIN_ OM_SHIFT = 0.001 TOP_________> 190 675 OPTIMIZE SCHEDULE_STEP = 1 preppdf_457W> Both soft sphere and statistical potential terms selected. pair4___223E> Array too small. Increase MPAIRS current maximum, current need: 33600 33600 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 14325865 13990. Starting time : 2002/09/05 09:56:49. Closing time : 2002/09/05 09:57:00. Total CPU time [seconds] : 11.04

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low sequence identity
by Margot Ernst 05 Dec '02

05 Dec '02

Dear Modeller support, I am modeling at low sequence identity and I believe to have the following problem: The homologous scaffold (comprising a core of beta strands) of my target, after a fisrt round of modeling, displays a (suspiciously) low RMSD with respect to the template, and a LOT of bad contacts involving the hydrophobic core. Consequently I think that in my target secondary structure motifs should be arranged more spaciously. How can I accomplish this in terms of additional modeling restraints, or chopping up the alignment and modeling in pieces, or whatever will work? thanks, margot

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restraining sec. structure elements
by Frank J A B 04 Dec '02

04 Dec '02

Dear All I have a theoretical model structure in hands with some regions structurally meaningful and others not. I'd like to use Modeller to modify only some regions of this model, I mean, those elements of sec. structure that looks like an helix but have some distortions on it. I guess that some EM/MD steps in Modeller could fix that. Would be nice if Modeller could re-design these regions considering the presence of the rest of the protein (without modifying obviously the rest of the model - only the chosen elements). I was looking through the manual and tutorials but couldn't find nothing very helpful. Any hont will be very welcome. Frank Alarcon www.lncc.br

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