December 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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Hai regarding ali file
by R Senthil Kumar 22 Dec '01

22 Dec '01

Dear modellers, I kindly request any one of you to send the example ali file for model building to build homodimer molecule along with heteroatoms. I mainly want to know sequence:1fdx: 1 : : 54 : :ferredoxin:Peptococcus aerogenes:-1.00:-1.00 how this line will look like when modelling homodimer template along with heteroatoms.Please help me in this regard. friendly from, Senthil kumar.R R.Senthil Kumar, Junior Research Fellow(JRF), c/o Dr.Akash Ranjan, Computational & Functional Genomics Group, Center For DNA Fingerprinting(CDFD), Hyderabad-500 076 Ph:040-7151344-Extn(Lab:1304) (Hostel:2300) E-mail:skumar@www.cdfd.org.in

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about restraints
by Paola D'Alessio 14 Dec '01

14 Dec '01

Dear modellers, I'd like to use the "make_restraint" command in my top file, in order to obtain five models that have a b-sheet in a particular region, but it doesn't work, in the final five models (after doing 100 cicles of VTFM) the b-sheet disappears (and the two strands too), while it is present in the .ini file, please, can you tell me something about this problem? the top file I used is the following: INCLUDE SET ALNFILE = 'align.ali' SET KNOWNS = 'E1' 'M1' ' SET SEQUENCE = 'abs' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '148:' '150:' MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '158:' '160:' #antiparallel sheet MAKE_RESTRAINTS RESTRAINT_TYPE = 'SHEET', ATOM_IDS = 'N:148' 'O:160', SHEET_H-BONDS = -5 RETURN END_SUBROUTINE -- dott. Paola D'Alessio Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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segmentation fault in Linux
by Rockey, William 13 Dec '01

13 Dec '01

Hi, Has anyone had trouble with Modeller crashing with segmentation faults under RedHat Linux 7.0? The specific error message is /usr/local/bin/modeller4/bin/mod4: line 39: 3410 Segmentation fault (core dumped) /usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF >$LOGF The log file has a 0 byte size when this occurs. I've tried setting the stacksize up to 512M, but this doesn't help. Both the MAXSEQ=6 and MAXSEQ=10 versions of the executables have the problem. The problem occurs both with my own job that I set up and the example file ./examples/tutorial-model/model-fast.top. Thanks in advance for any advice! Bill Rockey

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modeling problem
by Stephane Vandevuer 11 Dec '01

11 Dec '01

Hi, I'm performing homology modelling with Modeller. My template file is a Ca-only file, but this doesn't seem to be a problem. The .ini, .rsr and .sch files are correctly generated and the optimization begins for the first model (.D00000001) but does not succeed. Here is the end of the .log file : TOP_________> 327 234 OPTIMIZE pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 89694 89694 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I do search a little bit for the MPAIRS variable but I don't find it. Furthermore I was already successfull in modeling systems larger than the one I'm working now. Thanks for any help. Stephane.

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MALIGN3D
by Dan Thomas Major 10 Dec '01

10 Dec '01

I'm trying to align the structures that modeller produces by using the following top script: SET ATOM_FILES = 'hp2y1.B99990001' 'hp2y1.B99990002' 'hp2y1.B99990003' ; 'hp2y1.B99990004' 'hp2y1.B99990005' SET WRITE_FIT = on SET MAXRES = 2000 MALIGN3D Modeller gives an error: malign3_327W> Only one structure; nothing done. How can I tell modeller to align the structures even if they are the same? Thanks, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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loop refinement
by Paola D'Alessio 10 Dec '01

10 Dec '01

Hi, I'd like to refine two segments of the model I built by the loop refinement procedure, according to FAQ3 in the manual (version 4) the top file I used was: INCLUDE SET SEQUENCE = 'BRB2' SET MODEL = 'BRB2.ini' #initial model SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL = 1 SET ENDING_MODEL = 50 SET MD_LEVEL = 'refine1' SET RAND_SEED = -34871 CALL ROUTINE = 'loop' #cluster the models CALL ROUTINE = 'cluster', ID1 = STARTING_MODEL, ID2 = ENDING_MODEL SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT = '66:' '72:', SELECTION_STATUS = 'initialize' PICK_ATOMS SELECTION_SEGMENT = '242:' '258:', SELECTION_STATUS = 'add' RETURN END_SUBROUTINE ----------------------- I got the following message in the log file: TRANSFER RESIDUE NUMBERS AND CHAIN ID FROM MODEL2 TO MODEL: (ALIGNMENT = model2(1st in aln), model(2nd in aln)) # ALGNMT CODE ATOM FILE 1 BRB2 2 BRB2 END OF TRANSFER OF RESIDUE NUMBERS errdih__E> SIZE1*SIZE2 = 0 1 33 LYS errdih__E> SIZE1*SIZE2 = 0 1 34 SER errdih__E> SIZE1*SIZE2 = 0 1 35 SER errdih__E> SIZE1*SIZE2 = 0 1 36 CYS errdih__E> SIZE1*SIZE2 = 0 1 67 ASN can you explain what this message mean and how is important for the final models? thanks a lot, Paola -- dott. Paola D'Alessio Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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[Fwd: "MODELLER SUPPORT": Re: Adding missing coordinates]
by Andras Fiser 06 Dec '01

06 Dec '01

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Force constant
by Paolo Daniele 06 Dec '01

06 Dec '01

MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, I'd like to build 5 models of my protein with a b-strand in a specific region. After doing the VTFM optimization the b-strand disappears in all the models. How can I do to mantain this b-strand? I'd like to apply a force costant on the C-alpha carbons in that region while refinining the 5 models, the "MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND'" command didn't work!! Thanks in advance for your help. Best regards, Paolo Daniele ____________________________________________________________ Nokia 5510 insolito ma geniale. Vai a http://it.promotions.yahoo.com/nokia/ scoprilo e vincilo. Il concorso termina il 16 dicembre 2001.

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Adding missing coordinates
by Dan Thomas Major 06 Dec '01

06 Dec '01

I want to add missing coordinates to a pdb template file before using it for modelling, but I'm not succeeding! I would greatly appreciate some help. Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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