Sun Oct 9 08:15:09 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:15:09 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6324953 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 0.6324953 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2617 net assigned charge : 5.906005 assigned positive charge : 408.8326 centred at (gu) : 90.40740 89.56808 88.47395 assigned negative charge : -402.9274 centred at (gu) : 90.59446 89.55723 88.52513 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7498 nv = 96 ne = 84 npr = 56192 no. pairs analyzed = 56192 no. exposed pairs = 3351 no. arc points = 23582 no. surface atoms = 1134 nbur = 1621 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 4164 m= 0 mr = 32 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2285 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8981 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6564675E-08 1.4240553E-09 midg,1,midg; midg,igrid,midg 6.3991363E-09 7.2920692E-09 1,midg,midg; igrid,midg,midg 2.2812893E-08 -1.2993243E-08 gauss-seidel spectral radius is 0.9870677 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 08:15:10 rms-change max change #iterations 0.1429694 19.96100 at 10iterations 1.4027084E-02 2.201653 at 20iterations 1.3726507E-03 0.1929321 at 30iterations 1.3962154E-04 1.7457962E-02 at 40iterations 1.7869521E-05 2.3765564E-03 at 50iterations finished qdiffx linear iterations at : 08:15:12 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.7869521E-05 2.3765564E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:15:13 3.489u 0.250s 0:04.12 90.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:15:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.897486 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 1.897486 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2617 net assigned charge : 5.906005 assigned positive charge : 408.8326 centred at (gu) : 91.22142 88.70376 85.42110 assigned negative charge : -402.9274 centred at (gu) : 91.78313 88.67139 85.57521 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23582 grid for indexing accessible points = 1.400000 m= 29985 mr = 57093 m= 4322 mr = 21841 m= 245 mr = 2418 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.5800000 number of dielectric boundary points 34443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20595 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6324953 object centre at (A) : 73.44250 52.51000 37.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4442071E-02 -9.3391035E-03 midg,1,midg; midg,igrid,midg 9.9301599E-03 9.0780305E-03 1,midg,midg; igrid,midg,midg 6.5854572E-02 -5.0900225E-03 gauss-seidel spectral radius is 0.9986477 estimated iterations to convergence 215 setup time was (sec) 0.8900000 now iterating at: 08:15:14 rms-change max change #iterations 4.336562 214.6708 at 10iterations 2.036103 63.87646 at 20iterations 0.9533595 28.25483 at 30iterations 0.4489065 14.27190 at 40iterations 0.2109302 5.956331 at 50iterations 9.8977171E-02 3.010536 at 60iterations 4.6479385E-02 1.398333 at 70iterations 2.1881539E-02 0.6602783 at 80iterations 1.0268471E-02 0.3306389 at 90iterations 4.8422669E-03 0.1372967 at 100iterations 2.2816863E-03 7.0545197E-02 at 110iterations 1.0715602E-03 3.1093597E-02 at 120iterations finished qdiffx linear iterations at : 08:15:21 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 1.0715602E-03 3.1093597E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 08:15:22 8.204u 0.270s 0:08.91 95.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:15:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.846229 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 2.846229 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2617 net assigned charge : 5.906005 assigned positive charge : 408.8326 centred at (gu) : 91.83195 88.05553 83.13161 assigned negative charge : -402.9274 centred at (gu) : 92.67451 88.00699 83.36264 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 188272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23582 grid for indexing accessible points = 1.400000 m= 96668 mr = 138802 m= 35167 mr = 78593 m= 7506 mr = 27838 m= 1040 mr = 5201 m= 65 mr = 604 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 764 time to turn everything in is 1.450000 number of dielectric boundary points 77660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 20933 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.897486 object centre at (A) : 73.44250 52.51000 37.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1322954 -0.1281927 midg,1,midg; midg,igrid,midg 8.3545903E-03 7.5133368E-02 1,midg,midg; igrid,midg,midg 0.6392494 1.6231846E-02 gauss-seidel spectral radius is 0.9992713 estimated iterations to convergence 292 setup time was (sec) 1.760000 now iterating at: 08:15:24 rms-change max change #iterations 10.44423 399.1539 at 10iterations 6.227298 141.8836 at 20iterations 3.669409 81.30209 at 30iterations 2.157248 45.92105 at 40iterations 1.262296 30.08217 at 50iterations 0.7371664 14.06439 at 60iterations 0.4282938 7.909590 at 70iterations 0.2492553 4.506482 at 80iterations 0.1445722 2.808458 at 90iterations 8.3977327E-02 1.478736 at 100iterations 4.8598405E-02 0.8586216 at 110iterations 2.8128318E-02 0.4908142 at 120iterations 1.6284572E-02 0.2987995 at 130iterations 9.4184270E-03 0.1797543 at 140iterations 5.4377206E-03 9.4614983E-02 at 150iterations 3.1406898E-03 6.4202309E-02 at 160iterations 1.8166529E-03 3.0855179E-02 at 170iterations 1.0493990E-03 1.8218994E-02 at 180iterations finished qdiffx linear iterations at : 08:15:35 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.0493990E-03 1.8218994E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 08:15:35 12.653u 0.262s 0:13.38 96.4% 0+0k 0+0io 0pf+0w