modeller_usage October 2002

modeller_usage@salilab.org

30 participants
42 discussions

modeller installation on XP
by g e 25 Oct '02

25 Oct '02

just wanted to give my directions for installing modeller on XP: 1) get your code and everything 2) open your system>advanced>environmental variables control panel 3) add a new variable for each line of the modenv.bat file, with the variable being the part before the "=" and the value being the part after the "=" 4) EXCEPT for the path line, whose value should be added to the existing path value (after a semicolon) and excluding the redundant calling of the existing path information works fabulously now, if only i could really figure out how to use it. my practically zero unix experience makes even understanding the manual a bit of a pain in the ass. i guess i'm a loser for liking my GUI's or something... ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com

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Re: <no subject>
by Bozidar Yerkovich 25 Oct '02

25 Oct '02

I wrote Installation script for tcsh. Bash definitions are little bit different... Best, Bozidar > Dear Bozidar, > > Thanks for your answer. Currently, I´m using bash as shell not cshrc > because is the default shell in Linux. But I will try to install the > soft using the cshrc. However, I have checked the .bashrc file and > the "export" and "$PATH" are fine. > Regards, > >> >> It's probably permissions problem. It's hard to guess. I suggest > erase the >> current installation, and install locally as user. Make sure to source >> .cshrc file... >> >> Good luck, >> Bozidar >> >> >>> Dear Bozidar, >>> >>> I have installed the software in a PIII 700 (256 RAM) running > Slackware >>> Linux but I have got problems running modeller with not root user. I >>> have received the following: >>> >>> ?FORTRAN Runtime Error: >>> ?Bab file specification >>> ?OPEN(UNIT=11.... >>> >>> However, with root user I haven't received any error and I have > installed >>> the soft as user as root but I received the same error. Where is the >>> problem? >>> Regards, >>> >> -- >> Bozidar Yerkovich, PhD >> Rockefeller University >> New York, NY, 10021, USA >> 212-327-7206 >> bozidar(a)salilab.org >> http://salilab.org/modeller >> >> >> > > > Fernando Gabriel Ranea > > fgranea(a)microbiologia.org.ar > http://www.microbiologia.org.ar -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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Re: Problem in MODELLER6v2 installation
by Bozidar Yerkovich 25 Oct '02

25 Oct '02

Mea culpa. I should have made it more clear on the web page that those instructions do not apply to Win exec. There is a readme file in the root dir, after you unzip MOD for Win. Also please see my response from yesterday in the modeller_usage archives. Good luck, Bozidar > Dear Dr. Bozidar Yerkovich > Firstly, Thank you very much for KEY_MODELLER6v2 > I have some problem in program installation. I used Window XP. > After I followed the installation instruction on the web page and readme, I > still can not run the programme. > Could you please suggest more in detail. > Thanks in advanced > Best regards > Theeraphon Piacham > -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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Re: <no subject>
by Bozidar Yerkovich 25 Oct '02

25 Oct '02

It's probably permissions problem. It's hard to guess. I suggest erase the current installation, and install locally as user. Make sure to source .cshrc file... Good luck, Bozidar > Dear Bozidar, > > I have installed the software in a PIII 700 (256 RAM) running Slackware > Linux but I have got problems running modeller with not root user. I > have received the following: > > ?FORTRAN Runtime Error: > ?Bab file specification > ?OPEN(UNIT=11.... > > However, with root user I haven't received any error and I have installed > the soft as user as root but I received the same error. Where is the > problem? > Regards, > -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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Re: MODELLER (Win XP)
by Bozidar Yerkovich 24 Oct '02

24 Oct '02

Hi, I apologize for the confusion. MODELLER for Win doesn't use installation script. Instructions how to install it are given in the readme file that you will find in the root directory. I am also enclosing recent post from the list . Best, Bozidar > Dear Bozidar, > > I downloaded modeller6v2.zip for Win XP, but after unzipping I can't find an > installation script file in directory ./modeller6v2. Could you help in this > case? > > Yours sincerely, > > Alexander Petrenko > The University of Alabama > (Kevin Redding lab) > > > -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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Redhat 8.0 Error
by Bradley J. S. C. Olson 23 Oct '02

23 Oct '02

Hello I downloaded modeller6v2 and 6v1. Both packages run correctly on a SGI (IRIX 6.5), but when I install them on a Redhat linux box I get an error message at the welcome screen that says "Illegal instruction" and then the program exits. Has anyone else seen this before? Is there a fix? Thanks for you help! Brad Olson Michigan State University Plant Research Lab

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Fwd:
by Santiago Ramon 23 Oct '02

23 Oct '02

>Dear modellers, > >I've succesfully modelled a dimer with MODELLER 6. Now, I would like to >put the substrates in my model and optimize the interactions, but I might >be doing something wrong. I've initially placed the substrates (one per >subunit) as they are located at the template, and I'm using the following >alignment and top files: > >ALINGMENT: The template pdb corresponds to a dimer with two AMPPNP >molecules (one per subunit). The target sequence has been written twice to >align it with the two subunits of the template. > > >P1;ag_anp >structureX:ag_anp:1:A:518:A >MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPV--- >KKKNGLRVTPADQIDIIT-GALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQL >DEELGHVGLAQPGSPKLINSLLENG----YLPVVSSIGVTDE------GQLMNV >NADQAATALAATLGA-DLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVK >VNAALDAARTLGR-----PVDIASWRHAEQLPALFNGMPMGTRILA------. >/ >MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPV--- >KKKNGLRVTPADQIDIIT-GALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQL >DEELGHVGLAQPGSPKLINSLLENG----YLPVVSSIGVTDE------GQLMNV >NADQAATALAATLGA-DLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVK >VNAALDAARTLGR-----PVDIASWRHAEQLPALFNGMPMGTRILA------.* > >P1;akIII >sequence:akIII:1::502 >MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVR---LVVLSASAGITNLLVALAEGLEPGE >/-------SPALTDELVSH-GELMSTLLFVEILRER-DVQAQW-F----DVRKVMRT >NDRFGRAE---PDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRG >GSDYTAALLAEALHASRVDIWTDVPGIY--TTDPRVV-SAAKRIDEIAFA-EAAEMATF >GAKVLHPATLLPAVRSDIPVFVGSSKD----PRAG-----GTLVCNKTENPP. >/ >MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVR---LVVLSASAGITNLLVALAEGLEPGE >/-------SPALTDELVSH-GELMSTLLFVEILRER-DVQAQW-F----DVRKVMRT >NDRFGRAE---PDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRG >GSDYTAALLAEALHASRVDIWTDVPGIY--TTDPRVV-SAAKRIDEIAFA-EAAEMATF >GAKVLHPATLLPAVRSDIPVFVGSSKD----PRAG-----GTLVCNKTENPP.* > > >TOP FILE: an initial model named ter_anp.pdb is given as the starting >model. A subroutine is included to restrain the same changes in both subunits > >INCLUDE # Include the predefined TOP routines >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ALNFILE = 'dimer_anp.ali' # alignment filename >SET KNOWNS = 'ag_anp' # codes of the templates >SET SEQUENCE = 'akIII' # code of the target >SET ATOM_FILES_DIRECTORY = '.' # directories for input atom files > >SET MODEL = 'ter_anp.pdb' , GENERATE_METHOD = 'read_xyz' > >SET STARTING_MODEL= 1 # index of the first model >SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > >SET HETATM_IO = on >CALL ROUTINE = 'model' # do homology modelling > >SUBROUTINE ROUTINE = 'special_restraints' > > SET RES_TYPES = 'ALL' > SET ATOM_TYPES = 'ALL' > SET SELECTION_STATUS = 'INITIALIZE' > SET SELECTION_SEARCH = 'SEGMENT' > > SET SYMMETRY_WEIGHT = 0.5 > PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:''251:' > PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '252:''502:' > DEFINE_SYMMETRY ADD_SYMMETRY = on off > > > RETURN >END_SUBROUTINE > > >The log file gives the following error: > >preppdf_203E> CHARMM atom type is out of range; > Probably because GENERATE_TOPOLOGY was not called. > Atom index, atom type: 0 >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > >I would be very thankful if anyone could tell me what I am doing wrong and >if there is a better strategy to do it. > >Many thanks in advance Santiago

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modeller
by somanadh 23 Oct '02

23 Oct '02

I am using modeller6v2 and ran the command ./mod6v2 model-default.top. The process stopped after a couple of seconds. the model-default.log file says file not found: 'alignment.ali'. the file exists in the same directory as model-default.top what is the problem? somanadh

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Installation problems Windows XP
by Simon P Gough 21 Oct '02

21 Oct '02

Dear Modellers & Bozidar & team (Sending against think it got lost) Thanks for sending the key for the program . As a computer illiterate I find it hard to understand how to install modeller under Windows XP (1.7GHz Athlon processor, 1.5mB RAM) using the instructions given on the Web site. After unpacking the zip file to C:\ Modeller6v2 Then I setenv "KEY_MODELLER6v2" to "E-mailed value" setenv MODINSTALL6v2 C:\modeller6v2 Why ? setenv LIBS_LIB6v2 $MODINSTALL6v2/models.lib (I guessed it might be this one ??) set path=($path $MODINSTALL6v2) OK -left out the non-existent "bin" directory ?? set limit stacksize unlimited Not accepted by program -not done I could not then run the program with the command "Install" or "modeller6v2.exe" Or "make install" Could anyone please help me . It would be great to be able to use this program. Thanks! Simon Gough

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Is this a bug?
by Richard Friedman 21 Oct '02

21 Oct '02

Dear Modellers, When running the compare.log script on the TvLDH example I obtained a qualitatively different aliignment than the "known" which I downloaded from the web-site. Here is an excerpt the compare.log file from the web-site , at line 442. 80 0.310 0.106 A 80 L 80 L 80 V 123 81 0.180 0.050 * D 81 D 81 D 81 D 124 82 0.212 0.039 Y 82 V 82 V 82 W 125 83 0.206 0.047 * A 83 A 83 A 83 A 126 84 0.165 0.073 L 84 I 84 I 84 L 127 85 0.122 0.037 * L 85 L 85 L 85 L 128 86 0.158 0.052 V 86 V 86 V 86 I 129 87 0.347 0.031 * G 87 G 87 G 87 G 130 88 0.609 0.174 A 88 S 88 S 88 A 131 # ============================================= 89 1.375 0.314 P 90 M 89 M 89 P 133 # ============================================= 90 1.479 0.649 R 97 L 100 D 99 R 140 # ============================================= 91 1.463 0.278 V 103 A 103 A 103 I 146 92 0.782 0.226 * N 104 N 104 N 104 N 147 93 1.087 0.426 G 105 V 105 V 105 G 148 94 0.845 0.340 K 106 K 106 K 106 Q 149 95 0.411 0.068 * I 107 I 107 I 107 I 150 96 0.386 0.096 * F 108 F 108 F 108 F 151 97 0.542 0.245 T 109 K 109 K 109 A 152 98 0.478 0.214 E 110 C 110 C 110 D 153 99 0.216 0.029 * Q 111 Q 111 Q 111 Q 154 Here is the same region of the file from my own run: 80 0.312 0.109 A 80 L 80 L 80 V 123 81 0.185 0.053 * D 81 D 81 D 81 D 124 82 0.216 0.042 Y 82 V 82 V 82 W 125 83 0.209 0.049 * A 83 A 83 A 83 A 126 84 0.167 0.075 L 84 I 84 I 84 L 127 85 0.126 0.040 * L 85 L 85 L 85 L 128 86 0.163 0.054 V 86 V 86 V 86 I 129 87 0.349 0.027 * G 87 G 87 G 87 G 130 88 0.610 0.174 A 88 S 88 S 88 A 131 # ============================================= 89 1.383 0.320 P 90 M 89 M 89 P 133 # ============================================= 90 1.481 0.649 R 97 L 100 D 99 R 140 # ============================================= 91 1.160 0.416 L 101 K 102 K 102 L 144 # ============================================= 92 1.456 0.284 V 103 A 103 A 103 I 146 93 0.776 0.235 * N 104 N 104 N 104 N 147 94 1.083 0.431 G 105 V 105 V 105 G 148 95 0.840 0.344 K 106 K 106 K 106 Q 149 96 0.407 0.072 * I 107 I 107 I 107 I 150 97 0.380 0.101 * F 108 F 108 F 108 F 151 98 0.536 0.252 T 109 K 109 K 109 A 152 If I understand the output correctly the gap structure of the alignments is different between the two runs. I will be sending my directory contents under separate cover. I would greatly appreciate your input as to whether this discrepancy is due to A. Numerical differences between running the program on different machines. B. A problem with the Version for the Alpha. C. A problem with my installation of the Alpha Version. D. An error on my part running the program. Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.ccc.columbia.edu http://cancercenter.ccc.columbia.edu/~friedman/ In Memoriam, Robert Kanigher

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modeller_usage October 2002