- modeller_usage - salilab.org

top files for ligands
by Oliver Hucke 08 Oct '03

08 Oct '03

Hi there, I am about to make a homology model of a protein with a bound substrate molecule. I would like to consider electrostatic interactions during the model refinement which means that I need a topology file for the substrate. Is somebody aware of a program that can create a charmm top file for a small organic molecule starting from the pdb file? I know that Quanta can do this but don't have access to this program. I am looking for a non-commercial program. Thanks in advance! Best, Oliver _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________________

1 0

Alignment
by Gianluca Ottolina 08 Oct '03

08 Oct '03

Dear Modeller user, as a newcomer I have some questions about the alignment. I use Modeller to find structure and sequence related to the target sequence as described in the chapter 1.71 of the manual (SEQUENCE_SEARCH). I obtained five new file ( .tmp; .ali; .pap; .log; and .mat) and as suggested I check for the Z-score and I find five sequence with the score more than 4. Now I would like to use these five sequence to do the alignment as suggested in the chapter 1.7.2. Is Modeller able to calculate the alignment? Yes, I think. Now the real question is how to do this alignment with ALIGN, ALIGN2D, MALIGN and MALIGN3D. I try the example reported in the manual but something is wrong and the calculation aborted all the time. Can you please post another easy example of TOP file for ALIGN and comment it; the example in chapter 2.4.14 is not clear to me. How do I use the ( .tmp; .ali; .pap; .log; and .mat) file that I obtained previously? Thanx Gianluca -- Dr. Gianluca Ottolina Istituto di Chimica del Riconoscimento Molecolare CNR Via Mario Bianco 9, 20131 Milano Italy phone 0039 02 285 000 21 fax 0039 02 285 000 36 email gianluca.ottolina(a)icrm.cnr.it web www.icrm.cnr.it

1 0

Fwd: Help for "Sequence difference between alignment and pdb"
by Modeller Caretaker 27 Sep '03

27 Sep '03

Forwarding to list; please reply to original author. ----- Forwarded message from Dong Chen <dong.chen(a)usu.edu> ----- Subject: Help for "Sequence difference between alignment and pdb" Date: Fri, 26 Sep 2003 18:10:45 -0600 From: "Dong Chen" <dong.chen(a)usu.edu> To: <modeller-care(a)salilab.org> Hi, I am trying to model a protein by its own structural information, but it gives me "Sequence difference between alignment and pdb" error message in the log.file. Could somebody help to see where is problem. Attached are the files I used. Thanks, Dong ####1EDU.atm ####model-Peter.top: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment_Peter.ali' # alignment filename SET KNOWNS = '1EDU' # codes of the templates SET SEQUENCE = 'peter' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling ####alignment_Peter.ali: C; A sample alignment in the PIR format; used in tutorial >P1;1EDU structure:1EDU:2:A :150:A: : : : -NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR LREERAHALKTKEKLAQTATA* >P1;peter sequence:peter:1 : :150 : : : : : -NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR LREERAHALKTKEKLAQTATA* ####logfile.log: MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Windows_NT BTC101DC x86 Family 15 Model 1 Stepping 2, Genuin Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2003/09/23 17:56:59.346 TOP_________> 105 705 SET ALNFILE = 'alignment_Peter.ali' TOP_________> 106 706 SET KNOWNS = '1EDU' TOP_________> 107 707 SET SEQUENCE = 'peter' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL alignment_Peter.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 4458129 4353.642 4.252 openf5__224_> Open 11 OLD SEQUENTIAL alignment_Peter.ali read_al_374_> Non-standard residue type,position,sequence: X 29 1 read_al_374_> Non-standard residue type,position,sequence: X 46 1 read_al_374_> Non-standard residue type,position,sequence: X 48 1 read_al_374_> Non-standard residue type,position,sequence: X 67 1 read_al_374_> Non-standard residue type,position,sequence: X 70 1 read_al_374_> Non-standard residue type,position,sequence: X 89 1 read_al_374_> Non-standard residue type,position,sequence: X 29 2 read_al_374_> Non-standard residue type,position,sequence: X 46 2 read_al_374_> Non-standard residue type,position,sequence: X 48 2 read_al_374_> Non-standard residue type,position,sequence: X 67 2 read_al_374_> Non-standard residue type,position,sequence: X 70 2 read_al_374_> Non-standard residue type,position,sequence: X 89 2 Read the alignment from file : alignment_Peter.ali Total number of alignment positions: 149 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1EDU 149 1 1EDU 2 peter 149 1 peter TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1EDU.atm rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 29 24 UNK 11 MET PSSSLXSEIAD rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 4458129 4353.642 4.252 Starting time : 2003/09/23 17:56:59.346 Closing time : 2003/09/23 17:57:01.549 Total CPU time [seconds] : 1.72 ----- End forwarded message -----

3 2

Fwd: what is the problem?
by Modeller Caretaker 26 Sep '03

26 Sep '03

Forwarding to list. ----- Forwarded message from Yang Xiaolin <yangxl(a)pumc.edu.cn> ----- From: "Yang Xiaolin" <yangxl(a)pumc.edu.cn> To: "Modeller Caretaker" <modeller-care(a)salilab.org> Subject: what is the problem? Date: Sat, 27 Sep 2003 01:32:48 +0800 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Hi,all I used the following sentence in a cgi script written by Perl. system("mod all.top"); The error information is: sys_____214E> File probably does not exist. Perhaps you have to increase swap space size. Filename: 1064585746 Command : uname -rnsm > 1064585746 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 0 0.000 0.000 Starting time : 2003/09/26 22:15:45.975 Closing time : 2003/09/26 22:15:46.135 Total CPU time [seconds] : 0.07 The command "mod all.top" can run smoothly as command line or the script was not run through web. How can I resolve this problem? Thank you ! Sherin Yang ----- End forwarded message -----

1 1

Fwd: Re: model_refinement
by Modeller Caretaker 24 Sep '03

24 Sep '03

Forwarding to list. From: Denis Volkov <D.Volkov(a)artcustoms.ru> Subject: Fwd: Re: model_refinement ===8<==============Original message text=============== Hi, Oliver! First of all thank you for your help! I'll try to run Procheck on every template. As to alignment...automatic alignment produced by Modeller and ClustalW didn't satisfied me. The problem is that I'll try to model unknown retroviral aspartic protease and all enzymes of this class share a little similarity. So I used manually adjusted alignment based on knowledge of conserved regions of this class. No, I didn't used any restrains during all MD steps. I thought that this is a little bit unnatural to fix one region and don't other. But now I think that this may be a clue. But I have another question: If I've got so little similarity can I used a data of predicted secondary structure(I know that Modeller can do it)? Will it improve a quality of a model? Thanks in advance Denis Volkov Enzyme Laboratory,IBCH RAS -- Best regards, Denis mailto:themelon@yandex.ru ===8<===========End of original message text===========

1 0

Fwd: modelling problem
by Modeller Caretaker 24 Sep '03

24 Sep '03

Forwarding to list. ----- Forwarded message from sujata <sujataroy(a)hotmail.com> ----- From: "sujata" <sujataroy(a)hotmail.com> To: <modeller-care(a)salilab.org> Subject: modelling problem Date: Fri, 5 Sep 2003 09:56:35 +0530 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 I want to model a protein using only one template,because i have obtained significant sequence similarity with our query sequence. But i am having a different question. In the template there are three residues between two cosicutive structurally conserved region, where in the query sequence the gaps are inserted due to proper alignment. I am assigning coordinates to the structurally conserved region, thus there is a gap in my model protein. how can i solve this problem? can any one help me? ----- End forwarded message -----

1 0

Array too small
by Pedro Antonio Reche 23 Sep '03

23 Sep '03

HI, I am trying to create a 223 residue model using modeller, and I got the follwing error: pick_re_612_> Number of MODEL atoms, selected restraints; 1916 18082 TOP_________> 295 234 OPTIMIZE pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 5748 5748 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 11972385 11691.782 11.418 Starting time : 2003/09/23 13:52:56.775 Closing time : 2003/09/23 13:53:22.068 Total CPU time [seconds] : 25.00 I am using modeller6v2 in a linux box, I have never seen this error before, and therefore I will appreciate any help or suggestion to solve this problem. Regards, Pedro

1 0

solvent accessibility & WRITE_DATA
by Oliver Hucke 18 Sep '03

18 Sep '03

Dear Modeller users & developers, I would like to use the capability of modeller to calculate different kind of solvent accessibility data with the WRITE_DATA command. I can get the *.psa file and the *.sol file using the script shown below (practically identical with the example in the manual). Now my questions: o what are the units of the numbers given in the *.psa file? I suppose that the "Sum" coloumns give the accessible surface in square Angstrom. The "Per." coloumns are supposed to the accessible surface area in percent of the total surface? Why do I get values above 100 in many cases then? o How should the ACCESSIBILITY_TYPE parameter of WRITE_DATA be used to write different kind of accessibility dat to the Biso coloumn of the *.sol file? As far as I understand the manual the ACCESSIBILITY_TYPE parameter can be used to influence this part of the *.sol output file? I tried various things without any effect. o What are the numbers written to the *.sol file with the script below? Thanks a lot in advance, Oliver ____________________________________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________ My input script: ------------------------------------------------------------ SET OUTPUT_CONTROL = 1 1 1 1 0 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off READ_MODEL FILE = 'protein' SET RADII_FACTOR = 1.0 WRITE_DATA FILE = 'protein', OUTPUT = 'PSA' -------------------------------------------------------------- Start of the protein.psa file: -------------------------------------------------------------- #COLUMNS S S S N N N N N N N N N N # produced by MODELLER # # File of summed (Sum) and % (per.) accessibilities # probe radius : 1.400 # integration step : 0.100 # water included : ? # hetatom included : ? # accessibility type : CONTACT # number of residues : 730 # # Res Res All atoms Non P side Polar Side Total Side Main Chain # Num type Sum Per. Sum Per. Sum Per. Sum Per. Sum Per. ACCESS 55 PHE A 75.12 123.5 50.74 98.4 0.00 0.0 50.74 98.4 24.38 262.7 ACCESS 56 LEU A 19.62 34.7 16.14 34.6 0.00 0.0 16.14 34.6 3.47 35.0 ACCESS 57 SER A 20.64 61.1 11.84 75.1 7.67 97.5 19.51 82.6 1.13 11.1 ACCESS 58 LEU A 3.76 6.6 2.99 6.4 0.00 0.0 2.99 6.4 0.76 7.7 ACCESS 59 ASP A 31.28 79.4 9.54 59.8 13.93 103.7 23.47 79.8 7.81 78.3 -------------------------------------------------------------------------------------------------- Start of the corresponding *.sol file: --------------------------------------------------------- # produced by MODELLER # # File of atomic accessibilities # probe radius : 1.400 # integration step : 0.100 # water included : ? # hetatom included : ? # accessibility type : CONTACT # number of residues : 730 ATOM 1 N PHE A 55 107.149 -1.404 53.483 1.650 14.140 ATOM 2 CA PHE A 55 106.564 -2.771 53.570 1.800 1.890 ATOM 3 C PHE A 55 106.502 -3.415 52.180 1.800 1.008 ATOM 4 O PHE A 55 107.505 -3.970 51.725 1.550 9.229 ATOM 5 CB PHE A 55 105.182 -2.745 54.253 1.800 2.554 ATOM 6 CG PHE A 55 105.162 -3.402 55.622 1.800 0.319 ATOM 7 CD1 PHE A 55 104.233 -4.411 55.914 1.800 7.619 ATOM 8 CD2 PHE A 55 106.077 -3.026 56.615 1.800 4.669 ATOM 9 CE1 PHE A 55 104.214 -5.040 57.174 1.800 11.557 --

1 0

Fwd: Re: model_refinement
by Modeller Caretaker 13 Sep '03

13 Sep '03

Forwarding to list. ----- Forwarded message from Denis Volkov <themelon(a)yandex.ru> ----- Date: Thu, 11 Sep 2003 14:15:18 +0400 From: Denis Volkov <themelon(a)yandex.ru> X-Mailer: The Bat! (v1.52f) Organization: IBCH To: modeller-care(a)salilab.org Subject: Re: model_refinement Hello,Oliver Thank you for fast answering! :) No i didn't test a quality of templates course i used 4 structures as a templates so its difficult to do it. Alignment I manually adjust so it's not a origin of fault. I look at the model again and think it's not so bad as I said. But a problem is more global: A similarity with templates is no more than 20%. A great deal of mismatches are in loop origin so it's not so bad...but can i do a good model with so low similarity? As I said I use Charmm, I used it to investigate protein-protein interactions. I used Modeller model to investigate enzyme-substrate and enzyme-inhibitor interaction. But after MD a structure was a great deal disturbed. Is it a problem of low similarity or as you said its not good to use MD with models maid by Modeller? Also I've another question: earlier I used Windows version of Modeller and everything was OK, but now I run Modeller on Linux and have some problem. When I used sequence-search routine it runs for some time (~30-40 min) but then terminated. In log file there is nothing interesting: chains libraries were opened two times. First times it takes 20Mb of memory, second time ~200 Mb and then it terminated. So the problem is a memory usage as I think. I looked through archive and find out that it's a common problem. I checked my top-files and system config (stack size) and everything is good. I've got 500 Mb RAM but half of it utilized by X-Windows. So may be i should run some Modeller routines without running X ? Thanks in advance Denis Volkov Enzyme Laboratory,IBCH RAS -- Best regards, Denis mailto:themelon@yandex.ru ----- End forwarded message -----

2 1

Fwd: Re: how to ERROR: MODEL atom not classified: TYR:OT1 TYR
by Modeller Caretaker 10 Sep '03

10 Sep '03

Forwarding to list. ----- Forwarded message from Darren Thompson <thompson(a)hydrogen.ucsc.edu> ----- Date: Wed, 10 Sep 2003 13:37:34 -0700 Subject: Re: how to ERROR: MODEL atom not classified: TYR:OT1 TYR From: Darren Thompson <thompson(a)hydrogen.ucsc.edu> To: Modeller Caretaker <modeller-care(a)salilab.org> X-Mailer: Apple Mail (2.552) does your template have dihydroxytyrosine, OT is not the standard pdb nomenclature for oxygen atoms. Maybe OT is oxygen terminal? Try editing the pdb file and remove the T On Wednesday, September 10, 2003, at 10:38 AM, Modeller Caretaker wrote: >Forwarding to list. > >----- Forwarded message from Sherin Yang <sherin(a)sina.com> ----- > >From: "Sherin Yang" <sherin(a)sina.com> >To: <modeller-care(a)salilab.org> >Subject: how to ERROR: MODEL atom not classified: TYR:OT1 TYR >Date: Wed, 10 Sep 2003 10:54:04 +0800 >X-Mailer: Microsoft Outlook Express 6.00.2800.1106 > >Hi, all > >I want to use Align2D to align a sequence with a structure with pdb >format. I can't get the proper result. The log file tell me the >following wrong: > >iatmcls_286W> MODEL atom not classified: TYR:OT1 TYR >iatmcls_286W> MODEL atom not classified: TYR:OT2 TYR > >Who can tell me how to resolve such problem? > >Thank you! > >Sherin Yang > > >----- End forwarded message ----- > > ----- End forwarded message -----

1 0