Mon Oct 10 09:17:15 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+sph.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 = amb.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 Mon Oct 10 2011 at 09:17:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1046 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7378544 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): -34.49400 3.722000 ymin,ymax (A): 15.18500 54.51300 zmin,zma (A): -4.278000 43.97000 x,y,z range (A): 38.21600 39.32800 48.24800 scale (grids/A): 0.7378544 object centre (A): -15.38600 34.84900 19.84600 number of atom coordinates read : 1046 total number of charged atoms : 920 net assigned charge : 2.500001 assigned positive charge : 144.5921 centred at (gu) : 90.77981 91.99700 88.52888 assigned negative charge : -142.0920 centred at (gu) : 90.79453 91.78819 88.76491 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4152 nv = 96 ne = 84 npr = 20394 no. pairs analyzed = 20394 no. exposed pairs = 1577 no. arc points = 11946 no. surface atoms = 518 nbur = 528 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 1941 m= 6 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.1200000 number of dielectric boundary points 2475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 895 ## 75 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 3958 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8193141E-07 -4.8734890E-08 midg,1,midg; midg,igrid,midg -3.5615926E-08 1.8484516E-07 1,midg,midg; igrid,midg,midg 3.8843545E-08 3.6833679E-08 gauss-seidel spectral radius is 0.9903299 estimated iterations to convergence 83 setup time was (sec) 0.3100000 now iterating at: 09:17:15 rms-change max change #iterations 0.1560053 34.72832 at 10iterations 1.9850375E-02 3.743052 at 20iterations 2.6004587E-03 0.4987488 at 30iterations 3.4751510E-04 5.6800842E-02 at 40iterations 4.5810768E-05 8.4972382E-03 at 50iterations finished qdiffx linear iterations at : 09:17:18 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.5810768E-05 8.4972382E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 09:17:19 3.347u 0.158s 0:03.78 92.3% 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 Mon Oct 10 2011 at 09:17:19 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1046 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.213563 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): -34.49400 3.722000 ymin,ymax (A): 15.18500 54.51300 zmin,zma (A): -4.278000 43.97000 x,y,z range (A): 38.21600 39.32800 48.24800 scale (grids/A): 2.213563 object centre (A): -15.38600 34.84900 19.84600 number of atom coordinates read : 1046 total number of charged atoms : 920 net assigned charge : 2.500001 assigned positive charge : 144.5921 centred at (gu) : 92.33965 95.99120 85.58663 assigned negative charge : -142.0920 centred at (gu) : 92.38358 95.36446 86.29472 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 42417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11946 grid for indexing accessible points = 1.400000 m= 15887 mr = 25607 m= 3501 mr = 11440 m= 383 mr = 2262 m= 17 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 565 time to turn everything in is 0.2400000 number of dielectric boundary points 22726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7331 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) : 0.7378544 object centre at (A) : -15.38600 34.84900 19.84600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7394475E-02 5.7581984E-03 midg,1,midg; midg,igrid,midg -1.5103528E-02 1.3275120E-02 1,midg,midg; igrid,midg,midg 2.9496443E-03 1.0881544E-02 gauss-seidel spectral radius is 0.9988284 estimated iterations to convergence 231 setup time was (sec) 0.4400000 now iterating at: 09:17:19 rms-change max change #iterations 3.297665 194.4424 at 10iterations 1.607773 69.66177 at 20iterations 0.7964229 34.43253 at 30iterations 0.3933924 16.16836 at 40iterations 0.1925488 7.196082 at 50iterations 9.5495090E-02 3.858109 at 60iterations 4.6961319E-02 1.931379 at 70iterations 2.3141870E-02 0.9667587 at 80iterations 1.1354926E-02 0.4707866 at 90iterations 5.6207604E-03 0.2517744 at 100iterations 2.7681857E-03 0.1162794 at 110iterations 1.3626566E-03 5.4978371E-02 at 120iterations finished qdiffx linear iterations at : 09:17:26 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.3626566E-03 5.4978371E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 09:17:27 7.646u 0.208s 0:08.45 92.7% 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 Mon Oct 10 2011 at 09:17:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1046 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.320345 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): -34.49400 3.722000 ymin,ymax (A): 15.18500 54.51300 zmin,zma (A): -4.278000 43.97000 x,y,z range (A): 38.21600 39.32800 48.24800 scale (grids/A): 3.320345 object centre (A): -15.38600 34.84900 19.84600 number of atom coordinates read : 1046 total number of charged atoms : 920 net assigned charge : 2.500001 assigned positive charge : 144.5921 centred at (gu) : 93.50953 98.98677 83.38004 assigned negative charge : -142.0920 centred at (gu) : 93.57533 98.04665 84.44209 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 97264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11946 grid for indexing accessible points = 1.400000 m= 47816 mr = 62308 m= 20682 mr = 37747 m= 6695 mr = 16807 m= 1444 mr = 5075 m= 192 mr = 979 m= 11 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2139 time to turn everything in is 0.7000000 number of dielectric boundary points 51075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 7360 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) : 2.213563 object centre at (A) : -15.38600 34.84900 19.84600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1345416 3.7702046E-02 midg,1,midg; midg,igrid,midg -8.8725179E-02 -2.8396298E-03 1,midg,midg; igrid,midg,midg -2.1959508E-02 5.4704711E-02 gauss-seidel spectral radius is 0.9993010 estimated iterations to convergence 298 setup time was (sec) 0.9200000 now iterating at: 09:17:28 rms-change max change #iterations 7.366165 264.0463 at 10iterations 4.334732 123.9042 at 20iterations 2.543623 65.86456 at 30iterations 1.491170 41.45140 at 40iterations 0.8696430 20.96620 at 50iterations 0.5090461 11.89846 at 60iterations 0.2962863 7.870634 at 70iterations 0.1728149 4.177649 at 80iterations 0.1004192 2.214178 at 90iterations 5.8476452E-02 1.441013 at 100iterations 3.4044180E-02 0.7774067 at 110iterations 1.9834595E-02 0.5187454 at 120iterations 1.1543643E-02 0.2944555 at 130iterations 6.7050946E-03 0.1454468 at 140iterations 3.9004607E-03 9.1751099E-02 at 150iterations 2.2698401E-03 5.1446915E-02 at 160iterations 1.3148451E-03 2.9958725E-02 at 170iterations 7.6728733E-04 1.6760826E-02 at 180iterations finished qdiffx linear iterations at : 09:17:39 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 7.6728733E-04 1.6760826E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 09:17:40 11.991u 0.205s 0:12.47 97.7% 0+0k 0+0io 0pf+0w