Tue Oct 11 06:37:01 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 Tue Oct 11 2011 at 06:37:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 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: 0.7068822 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 0.7068822 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 307.8420 centred at (gu) : 90.16080 90.52380 89.47116 assigned negative charge : -300.3422 centred at (gu) : 89.98225 90.49805 89.43916 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 40958 no. pairs analyzed = 40958 no. exposed pairs = 2441 no. arc points = 16817 no. surface atoms = 830 nbur = 1207 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3943 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2700000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7744 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2147023E-08 6.9997824E-08 midg,1,midg; midg,igrid,midg 4.5619881E-08 8.2275783E-08 1,midg,midg; igrid,midg,midg -2.2218510E-08 1.4945346E-07 gauss-seidel spectral radius is 0.9895632 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 06:37:02 rms-change max change #iterations 0.1958189 28.77101 at 10iterations 2.4056299E-02 3.092125 at 20iterations 3.0724439E-03 0.4659061 at 30iterations 4.2488618E-04 5.6102753E-02 at 40iterations 7.2335672E-05 9.1643333E-03 at 50iterations finished qdiffx linear iterations at : 06:37:05 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.2335672E-05 9.1643333E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 06:37:05 3.458u 0.178s 0:04.15 87.2% 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 Tue Oct 11 2011 at 06:37:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 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: 2.120646 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 2.120646 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 307.8420 centred at (gu) : 90.48235 91.57149 88.41341 assigned negative charge : -300.3422 centred at (gu) : 89.94700 91.49427 88.31760 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 29229 mr = 51962 m= 5615 mr = 22183 m= 567 mr = 3756 m= 18 mr = 321 m= 0 mr = 9 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 132 time to turn everything in is 0.6000000 number of dielectric boundary points 30324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15158 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) : 0.7068822 object centre at (A) : 1.873501 -8.792001 11.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3191749E-02 4.7625296E-02 midg,1,midg; midg,igrid,midg 4.8606773E-03 3.4440618E-02 1,midg,midg; igrid,midg,midg 1.8926784E-02 4.3303959E-02 gauss-seidel spectral radius is 0.9988253 estimated iterations to convergence 231 setup time was (sec) 0.8900000 now iterating at: 06:37:07 rms-change max change #iterations 4.499041 230.8208 at 10iterations 2.221153 92.44134 at 20iterations 1.098797 37.36931 at 30iterations 0.5453295 17.21726 at 40iterations 0.2704048 8.141878 at 50iterations 0.1336728 4.280993 at 60iterations 6.6474393E-02 1.950922 at 70iterations 3.2822087E-02 0.9679403 at 80iterations 1.6341843E-02 0.4965668 at 90iterations 8.1254235E-03 0.2500305 at 100iterations 4.0315520E-03 0.1164055 at 110iterations 2.0167546E-03 6.0224533E-02 at 120iterations finished qdiffx linear iterations at : 06:37:14 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.0167546E-03 6.0224533E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 06:37:14 7.978u 0.225s 0:08.70 94.1% 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 Tue Oct 11 2011 at 06:37:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.180970 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 3.180970 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 307.8420 centred at (gu) : 90.72359 92.35735 87.62009 assigned negative charge : -300.3422 centred at (gu) : 89.92046 92.24139 87.47653 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 168787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 91055 mr = 125183 m= 36946 mr = 75781 m= 10784 mr = 30521 m= 2200 mr = 8441 m= 315 mr = 1616 m= 28 mr = 240 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 1.820000 number of dielectric boundary points 68317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 15272 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) : 2.120646 object centre at (A) : 1.873501 -8.792001 11.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6709689 0.3820599 midg,1,midg; midg,igrid,midg 1.5639301E-02 0.2807988 1,midg,midg; igrid,midg,midg 0.3005873 0.3216031 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 2.120000 now iterating at: 06:37:17 rms-change max change #iterations 10.03855 362.7568 at 10iterations 5.903725 116.1543 at 20iterations 3.475478 81.85657 at 30iterations 2.038069 41.75102 at 40iterations 1.193807 21.72298 at 50iterations 0.6993727 12.49503 at 60iterations 0.4095569 8.339901 at 70iterations 0.2391444 4.154956 at 80iterations 0.1398219 2.648622 at 90iterations 8.1421144E-02 1.599777 at 100iterations 4.7643758E-02 0.9539938 at 110iterations 2.7864395E-02 0.5282645 at 120iterations 1.6315814E-02 0.2788200 at 130iterations 9.6312510E-03 0.1553497 at 140iterations 5.7544499E-03 0.1100559 at 150iterations 3.4660234E-03 6.5472603E-02 at 160iterations 2.1609089E-03 3.9634705E-02 at 170iterations 1.4062379E-03 2.5079727E-02 at 180iterations finished qdiffx linear iterations at : 06:37:28 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.4062379E-03 2.5079727E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 06:37:28 13.212u 0.234s 0:13.81 97.3% 0+0k 0+0io 0pf+0w