Re: [Apbs-users] ObjectMapLoadDXFile-Error
Biomolecular electrostatics software
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From: David G. <sd...@gm...> - 2009-05-05 14:11:50
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Hi Kurtis, This doesn't look like the same error, but I'm not certain what the cause exactly is. Can you try running the calculation directly from the command line? That would at least tell us if it's a problem with APBS or PyMOL. Regards, Dave On May 4, 2009, at 5:15 PM, Anderson, Kurtis wrote: > Hello, > > Yet another posting a DXfile error...sorry all. > > I've spent some time going through the board here, and I believe > I've done everything right by minimizing the path, eliminating > spaces, etc...but to no avail. I think the error is in the temp > assignment--maybe a quick tip will get me going, thanks. > > -Kurtis Anderson > > > > PyMOL>reinitialize > CmdLoad: "/Users/djroue/APBS/test2/1fas.pqr" loaded as "1fas". > APBS Tools: set pqr file to /Users/djroue/APBS/test2/1fas.pqr > cs [4, 3, 4] > finedim [54.762001037597656, 41.559899234771727, 53.782000541687012] > nlev 4 > mult_fac 32 > finegridpoints [129, 97, 129] > Maximum number of grid points exceeded. Old grid dimensions were > [129, 97, 129] > Fine grid points rounded down from [117, 87, 117] > New grid dimensions are [97, 65, 97] > APBS Tools: coarse grid: (59.095,41.560,57.429) > APBS Tools: fine grid: (54.762,41.560,53.782) > APBS Tools: center: (36.269,19.971,7.486) > APBS Tools: fine grid points (97,65,97) > ObjectMapLoadDXFile-Error: Unable to open file! > > > > ======================================================= > GENERAL INFO > ======================================================= > APBS 1.1.0 (Mac OS X Intel) > Mac OS X 10.4.11 > working directory: /Users/djroue/APBS/test2/ > > > APBS installed in: > /Applications/apbs-1.1.0/ > > > PyMOL installed in: > /Applications/PyMOLX11Hybrid.app/ > > > > ======================================================= > PyMOL APBS TOOLS > ======================================================= > MAIN > Choose externally generated PQR: > /Users/djroue/APBS/test2/1fas.pqr > > CONFIGURATION > Set grid - CLICKED > [ion] +1 = 0.150 > [ion] -1 = 0.150 > > APBS LOCATION > APBS binary location: > /Applications/apbs-1.1.0/bin/apbs > > TEMP FILE LOCATIONS > Temp PQR file: > /Users/djroue/APBS/test2/pymol-generated.pqr > > Temp PDB file: > /Users/djroue/APBS/test2/pymol-generated.pdb > > Temp DX file: > /Users/djroue/APBS/test2/pymol-generated.dx > > APBS input file: > /Users/djroue/APBS/test2/1fas.in.txt > > > > ======================================================= > APBS INPUT FILE (1fas.in.txt from PDB2PQR server) > ======================================================= > read > mol pqr 1fas.pqr > end > elec > mg-auto > dime 129 97 97 > cglen 63.1108 45.7300 61.4601 > fglen 57.1240 45.7300 56.1530 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 78.5400 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > write pot dx pot > end > elec > mg-auto > dime 129 97 97 > cglen 63.1108 45.7300 61.4601 > fglen 57.1240 45.7300 56.1530 > cgcent mol 1 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > pdie 2.0000 > sdie 2.0000 > srfm smol > chgm spl2 > sdens 10.00 > srad 1.40 > swin 0.30 > temp 298.15 > calcenergy total > calcforce no > end > print elecEnergy 2 - 1 end > quit > > > ======================================================= > PQR file: /Users/djroue/APBS/test2/1fas.pqr > ======================================================= > > REMARK 1 PQR file generated by PDB2PQR (Version 1.4.0) > REMARK 1 > REMARK 1 Forcefield Used: parse > REMARK 1 Naming Scheme Used: parse > REMARK 1 > REMARK 5 > REMARK 6 Total charge on this protein: 4.0000 e > REMARK 6 > ATOM 1 N THR 1 46.148 16.581 2.104 -0.3200 2.0000 > ATOM 2 CA THR 1 44.862 15.936 2.105 0.3300 2.0000 > ATOM 3 C THR 1 43.983 16.642 1.087 0.5500 1.7000 > ATOM 4 O THR 1 44.150 17.855 0.925 -0.5500 1.4000 > ATOM 5 CB THR 1 44.293 16.088 3.528 0.0000 2.0000 > ATOM 6 OG1 THR 1 45.409 15.915 4.403 -0.4900 1.4000 > ATOM 7 CG2 THR 1 43.175 15.110 3.826 0.0000 2.0000 > ... > ATOM 910 HD1 TYR 61 30.649 12.920 7.128 0.1250 1.0000 > ATOM 911 HB1 TYR 61 32.812 13.407 6.001 0.0000 0.0000 > ATOM 912 HB2 TYR 61 32.833 13.922 4.451 0.0000 0.0000 > ATOM 913 HH TYR 61 26.611 13.103 3.935 0.4350 1.0000 > HETATM 914 OH H2O 62 27.026 18.812 4.463 -0.7200 1.4000 > HETATM 915 HH1 H2O 62 27.025 19.769 4.172 0.3600 1.0000 > HETATM 916 HH2 H2O 62 26.191 18.671 4.995 0.3600 1.0000 > ... > HETATM 1226 OH H2O 166 29.627 27.168 24.722 -0.7200 1.4000 > HETATM 1227 HH1 H2O 166 29.614 27.412 23.752 0.3600 1.0000 > HETATM 1228 HH2 H2O 166 30.517 26.813 25.007 0.3600 1.0000 > > > > > > > Kurtis Anderson > Keck Fellow - Structural Biology in Biodefense > Graduate Student - Biophysics, Structural and Computational Biology > University of Texas Medical Branch > Galveston, TX, 77555-1131 > (409) 747-6815 work > (516) 661-3199 cell > kur...@ut... > ------------------------------------------------------------------------------ > The NEW KODAK i700 Series Scanners deliver under ANY circumstances! > Your > production scanning environment may not be a perfect world - but > thanks to > Kodak, there's a perfect scanner to get the job done! With the NEW > KODAK i700 > Series Scanner you'll get full speed at 300 dpi even with all image > processing features enabled. http://p.sf.net/sfu/kodak-com > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users David W. Gohara, Ph.D. Center for Computational Biology Washington University School of Medicine http://smackfumaster.com (My iPhone Apps) http://gohara.wustl.edu (My Personal Site) http://www.macresearch.org (Science on the Mac) 314-362-1583 (phone) 617-216-8616 (cell) Google Chat: sdg0919 iChat: sdg0919 |