- modeller_usage - salilab.org

Many templates/targets
by Cvetan Stojkoski 09 Jan '03

09 Jan '03

Hey Modeller users, I'm trying to model 400+ proteins based on ~100 templates. I have an alignmentfile of 1500+ sequences comprising of the templates, targets and others. ClustalW was used to align the sequences. I have a few problems. - The sequences in the alignment file do not match the aminoacids present in the pdb files. _Generally_ the pdb files contain more residues than specified in the aligned sequence. Therefore I have to either concatonate the pdb files or specify the residues in the appropriate residues in the alignment file. - The ID codes in the alignment file do not match the atom file names. - There is no "second" line in each entry in the alignment file. Although all this can be done manually, I can't help but wonder if there is a way to automate/expidate the process. A paper published by Sanhez and Sali (1998) mentioned perl script that allowed for rapid progress through the various steps involved with modelling. Suggestions will be most appreciated. Some of the pdb files are complexes. If it can be avoided I'd prefer not to use these structures . However if I do decide to use some of them, I plan to minimise the E via MD (cns) of the protein (minus the ligand) before using it as a template. What are people's thoughts about this? Many thanks

2 2

How to change a pdb file's chain id without renumbering the residues using Modeller?
by Kong Lesheng 07 Jan '03

07 Jan '03

Hi, I have successed done this under Modeller 4. But under Modeller 6v2, the old script doesn't work. My top file is as follow: READ_MODEL FILE = 'xenl.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = off WRITE_MODEL FILE = 'xenl.mol', HETATM_IO = on The log file reported that assgn___547E> Incorrect element type for variable: RENUMBER_RESIDUES Element, element type: OFF 4 Command line: RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = OFF assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I have checked the libary file top.ini in modeller4 and modeller6v2 about RENUMBER_RESIDUES. Under modeller4 , 64 LOGICAL RENUMBER_RESIDUES 1 on # whether to renumber residues from 1 to N Under modeller6v2, 41 INTEGER RENUMBER_RESIDUES 0 # starting residue index for renumbering residues Is it possible to change a pdb file's chain id without renumbering the residues ? Thank you very much! With best regards, Lesheng

1 0

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

1 0

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

2 1

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

1 0

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.

2 2

# 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

2 2

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

2 1

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

2 1

Bump checking with modeller
by Frank J A B 27 Nov '02

27 Nov '02

Dear All Is there some easy way to do a bump checking in a protein model ? I mean, can I freeze the backbone and ask Modeller to do a bump checking correction in all sidechains in the model ? Thanks in advance Frank Alarcon www.lncc.br

1 0