Sun Oct 9 13:02:05 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 Sun Oct 9 2011 at 13:02:05 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6828689 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 0.6828689 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.70918 90.87495 90.53986 assigned negative charge : -353.8496 centred at (gu) : 89.71743 90.99262 90.58250 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7570 nv = 96 ne = 84 npr = 46620 no. pairs analyzed = 46620 no. exposed pairs = 3014 no. arc points = 21353 no. surface atoms = 1015 nbur = 1342 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4152 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 3820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1995 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1215041E-08 8.4185769E-09 midg,1,midg; midg,igrid,midg 4.8807340E-08 -2.0115351E-08 1,midg,midg; igrid,midg,midg 2.5282949E-08 1.7624583E-08 gauss-seidel spectral radius is 0.9888614 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 13:02:06 rms-change max change #iterations 0.1797694 26.87025 at 10iterations 2.0847093E-02 2.671936 at 20iterations 2.7936739E-03 0.3704567 at 30iterations 5.9589709E-04 9.1880798E-02 at 40iterations 1.8550991E-04 2.9815674E-02 at 50iterations finished qdiffx linear iterations at : 13:02:09 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.8550991E-04 2.9815674E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 13:02:09 3.305u 0.190s 0:03.77 92.5% 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 13:02:09 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.048607 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 2.048607 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.12694 92.62427 91.61915 assigned negative charge : -353.8496 centred at (gu) : 89.15204 92.97771 91.74730 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21353 grid for indexing accessible points = 1.400000 m= 31435 mr = 55040 m= 5671 mr = 23470 m= 468 mr = 3641 m= 6 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 0.3900000 number of dielectric boundary points 34935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17549 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) : 0.6828689 object centre at (A) : 18.79450 11.88950 23.93350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9100394E-02 1.0306643E-02 midg,1,midg; midg,igrid,midg 1.4624751E-02 -3.2777824E-02 1,midg,midg; igrid,midg,midg 5.2593850E-02 -9.8416256E-04 gauss-seidel spectral radius is 0.9987951 estimated iterations to convergence 228 setup time was (sec) 0.6100000 now iterating at: 13:02:10 rms-change max change #iterations 4.655467 201.6973 at 10iterations 2.266107 79.37571 at 20iterations 1.110456 36.22671 at 30iterations 0.5435452 16.37776 at 40iterations 0.2665960 7.970271 at 50iterations 0.1307731 3.972757 at 60iterations 6.4227261E-02 1.818499 at 70iterations 3.1536181E-02 1.122627 at 80iterations 1.5634637E-02 0.4568276 at 90iterations 7.8132357E-03 0.2326992 at 100iterations 3.9638714E-03 0.1169891 at 110iterations 2.0745546E-03 6.4647675E-02 at 120iterations finished qdiffx linear iterations at : 13:02:17 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.0745546E-03 6.4647675E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 13:02:18 7.781u 0.201s 0:08.29 96.2% 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 Sun Oct 9 2011 at 13:02:18 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.072910 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 3.072910 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 88.69020 93.93617 92.42854 assigned negative charge : -353.8496 centred at (gu) : 88.72794 94.46650 92.62089 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21353 grid for indexing accessible points = 1.400000 m= 98272 mr = 132981 m= 39045 mr = 80573 m= 10497 mr = 31879 m= 1983 mr = 7938 m= 168 mr = 1462 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 2757 time to turn everything in is 1.050000 number of dielectric boundary points 78798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 17722 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) : 2.048607 object centre at (A) : 18.79450 11.88950 23.93350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3705274 -1.2196724E-02 midg,1,midg; midg,igrid,midg 0.3270035 -0.4249405 1,midg,midg; igrid,midg,midg 0.4821836 -0.1110469 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 1.300000 now iterating at: 13:02:19 rms-change max change #iterations 10.55919 415.4112 at 10iterations 6.246517 126.8210 at 20iterations 3.681023 68.73212 at 30iterations 2.168707 42.23867 at 40iterations 1.271577 24.70647 at 50iterations 0.7455018 15.34424 at 60iterations 0.4362654 7.308674 at 70iterations 0.2555661 4.537676 at 80iterations 0.1492236 2.566220 at 90iterations 8.7296322E-02 1.577202 at 100iterations 5.1094845E-02 0.8780289 at 110iterations 3.0035578E-02 0.4917164 at 120iterations 1.7737376E-02 0.3107576 at 130iterations 1.0649347E-02 0.2221375 at 140iterations 6.5603321E-03 0.1355190 at 150iterations 4.1984767E-03 8.7966919E-02 at 160iterations 2.8509640E-03 6.5570831E-02 at 170iterations 2.0664802E-03 4.4580460E-02 at 180iterations finished qdiffx linear iterations at : 13:02:31 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 2.0664802E-03 4.4580460E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 13:02:31 13.012u 0.239s 0:13.52 97.9% 0+0k 0+0io 0pf+0w