January 2004 - modeller_usage

Ligand parameters
by Thomas Duncan 20 Jan '04

20 Jan '04

I have been testing MODELLER with a ras-GDP template for inclusion of such a 'standard' nucleotide ligand as GDP. My most recent files are attached (.ali, .top, .log, and template/model pdb files). The problem: warnings (W>) in log file indicate lack of some parameters for GDP in the par.lib file, even though GDP is included as a residue in the res_type.lib. MODELLER adds some defaults values for the undefined parameters, but clearly does not handle the GDP accurately since, in the pdb model calculated, the guanine ring is nonplanar. I am not that familiar with the format of the par.lib file. Is there a reasonable way to add parameters to get the GDP ligand modeled properly? Thanks, Tom

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Re: [modeller_usage] The number of the models
by Thomas Duncan 20 Jan '04

20 Jan '04

I believe that, when MODELLER starts any partcular model (each from a different randomly perturbed version of the starting model (.ini), it will abort that model if the scoring function exceeds some upper limit. Thus, you may get fewer than the total models requested if this occurs. Best wishes, Tom Duncan >>> BinBin Liu 01/17/04 08:26AM >>> Dear Modellers, happy new year! I set the starting and ending model number 1 and 10 respectively. But modeller only wrote eight .B9999xxxx files to me. It is from .B99990002 to ..B99990009. Does anybody know the reasons? Many thanks! BinBin

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Re: the number of the models
by BinBin Liu 20 Jan '04

20 Jan '04

Hi, Ben Thank you first. The .top file is: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = ' ./ ' SET ALNFILE = '1bl8-kv14.ali ' SET KNOWNS = '1bl8.pdb' SET SEQUENCE = 'kv14' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 CALL ROUTINE = 'model' And the .ali is: >P1;1bl8.pdb structureX: 1bl8.pdb: 23: A: 119: D: : : : ALHWRAAG AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRC VAVVVMVAGITSFGLVTAALATWFVGREQ/ ALHWRAAG AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYP VTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQ/ ALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYP VTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQ/ ALHWRAAG AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYP VTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQ/* >P1;kv14 sequence: kv14: 474: A: 570: D: : : : RASMRELGLLIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYG DMKPITVGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYH/ RASMRELGLLIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYG DMKPITVGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYH/ RASMRELGLLIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYG DMKPITVGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYH/ RASMRELGLLIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYG DMKPITVGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYH/ * And in .log file there are ten models from B99990001 to B99990010. Many thanks BinBin

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when does MODELLER hang
by Jaimin Shah 20 Jan '04

20 Jan '04

Dear MODELLER users, Thank you for ur help so far. One problem still persists. MODELLER hangs at one point after some time: Dynamically allocated memory at amprmcns [B,kB,MB]: 17981749 17560. 301 17.149 openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr The TOP and ALI files are alright. Please solve my problem. Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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Simple and Multiple Alignment
by Hugo Brandão Uchôa 19 Jan '04

19 Jan '04

Dear Sir, I´m trying to perform two kinds of modelings: one with simple alignment (using one template) and another with multiple alignment (using 2 templates). However there is a problem in alignment step. I 've use d the follow file to perform alignment with 1 template: READ_MODEL FILE = '1hcl.pdb' SEQUENCE_TO_ALI ALIGN_CODES = '1hcl' READ_ALIGNMENT FILE = 'cdk10.seq', ALIGN_CODES = 'cdk10', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='1hcl-cdk10.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='1hcl-cdk10.pap', ALIGNMENT_FORMAT = 'PAP' Modeller performs the alignment with this file, but the result in PIR format is a file that contais just a piece of the sequence of template: structureX:1hcl*: 1 : : 81 : :undefined:undefined:-1.00:-1.00 MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRTEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLV FE* Is there some error in the top file??? I also need a example of a top file to perform a alignment with 2 templates. Could somebody help me??? Thank you. Hugo Brandão Uchôa São Paulo State University ______________________________________________________________________ Yahoo! GeoCities: a maneira mais fácil de criar seu web site grátis! http://br.geocities.yahoo.com/

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Hetatm-entries in calculated model
by Volker Aufschild 18 Jan '04

18 Jan '04

Dear Modeller-Users, Im not only new to this Newsgroup, but also fairly new to Modeller. Im using Modeller6v2 for a practical work at the University of Munich, Germany, doing a Homology Modelling approach. The problem weve ran into is, that in the calculated model-files .B999900xx we only have HETATM-Entries and no ATOM-Entries. That might be a simple problem, but I couldnt find a solution looking through the manual and faq. Were using a multiple alignment done by clustalw and the following simple .top-file: ############################################################# INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET OUTPUT_DIRECTORY = ...... SET DIRECTORY = ....... SET ALNFILE = ...... SET KNOWNS = ...... SET SEQUENCE = ....... SET ATOM_FILES_DIRECTORY = ........ SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' ##################################################################### I would be very pleased if someone could help me. Volker Aufschild --------------------------------------------------------------------- | Volker Aufschild | Lindwurmstr. 82 / Hochstr. 37 | 80337 München / 84066 Mall.-Pfaff. | mail: <mailto:volker@aufschild.de> volker(a)aufschild.de | Tel: 0170/7555737 | ICQ: 10202493 | MSN: <mailto:dmob_voder@hotmail.com> dmob_voder(a)hotmail.com

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The number of the models
by BinBin Liu 18 Jan '04

18 Jan '04

Dear Modellers, happy new year! I set the starting and ending model number 1 and 10 respectively. But modeller only wrote eight .B9999xxxx files to me. It is from .B99990002 to .B99990009. Does anybody know the reasons? Many thanks! BinBin

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Inserting Cl atoms
by rleite＠ualg.pt 18 Jan '04

18 Jan '04

Dear Modellers, I'm relatively new to Modeller, and I have a question which I hope has an easy answer. It's possible to insert to Cl and H2O atoms in the atom file of the known structure. Another question how can I use the energy command to determine the best possible structure?Thanks! Ricardo Leite rleite(a)ualg.pt -CCMAR- University of Algarve Faro - Portugal

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windows problem?
by Jaimin Shah 16 Jan '04

16 Jan '04

Dear all, A colleague of mine ran the same .TOP file in a Linux PC and it worked. As I am more conversant with Windows, please let me know what problem could be there that disables me from getting models (the problem previously posted)in it, i.e, it hangs at: openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr Sincerely, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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Can MODELLER use temperature B-factors?
by Karsten Suhre 16 Jan '04

16 Jan '04

Dear all, I have a simple question : Can MODELLER use the B-factors of in the template structures, e.g. to modify the weight given to different constrains? Thank you very much, Karsten (IGS-CNRS, Marseille, France).

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