Mon Oct 10 19:35:15 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 19:35:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6055245 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 0.6055245 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.499969 assigned positive charge : 391.8587 centred at (gu) : 90.61394 89.66321 90.76553 assigned negative charge : -395.3595 centred at (gu) : 90.69129 89.86424 90.83025 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6325 nv = 96 ne = 84 npr = 53394 no. pairs analyzed = 53394 no. exposed pairs = 3503 no. arc points = 24728 no. surface atoms = 1171 nbur = 1453 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3172 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2000000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2437 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7945823E-10 -5.5092353E-09 midg,1,midg; midg,igrid,midg 7.4443851E-09 -1.0023034E-08 1,midg,midg; igrid,midg,midg 1.3885880E-09 -5.9742855E-09 gauss-seidel spectral radius is 0.9858872 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 19:35:15 rms-change max change #iterations 0.1105677 19.09326 at 10iterations 9.4782691E-03 1.430355 at 20iterations 8.3126791E-04 0.1471729 at 30iterations 7.2578347E-05 1.0745049E-02 at 40iterations 6.5065087E-06 1.1520386E-03 at 50iterations finished qdiffx linear iterations at : 19:35:18 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 6.5065087E-06 1.1520386E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:35:19 3.433u 0.178s 0:04.25 84.7% 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 19:35:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.816574 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 1.816574 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.499969 assigned positive charge : 391.8587 centred at (gu) : 91.84120 88.98929 92.29595 assigned negative charge : -395.3595 centred at (gu) : 92.07361 89.59236 92.49044 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24728 grid for indexing accessible points = 1.400000 m= 22463 mr = 45234 m= 3114 mr = 15461 m= 167 mr = 1617 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1034 time to turn everything in is 0.3500000 number of dielectric boundary points 31657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19413 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) : 0.6055245 object centre at (A) : -0.6359997 35.77250 22.21750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1742950E-03 -1.0190580E-02 midg,1,midg; midg,igrid,midg 1.8266678E-02 -2.8211381E-02 1,midg,midg; igrid,midg,midg -3.2054933E-03 -5.2966187E-03 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 0.5600000 now iterating at: 19:35:20 rms-change max change #iterations 3.887549 172.1489 at 10iterations 1.748598 68.08210 at 20iterations 0.7845400 28.73680 at 30iterations 0.3553676 12.31677 at 40iterations 0.1600212 5.662552 at 50iterations 7.2332397E-02 2.576397 at 60iterations 3.2605816E-02 1.095622 at 70iterations 1.4742782E-02 0.5210457 at 80iterations 6.6588381E-03 0.2381210 at 90iterations 3.0044571E-03 9.9281311E-02 at 100iterations 1.3562298E-03 4.3540955E-02 at 110iterations 6.1194692E-04 2.2112370E-02 at 120iterations finished qdiffx linear iterations at : 19:35:27 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 6.1194692E-04 2.2112370E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 19:35:27 7.837u 0.198s 0:08.32 96.3% 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 19:35:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.724860 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 2.724860 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.499969 assigned positive charge : 391.8587 centred at (gu) : 92.76154 88.48380 93.44374 assigned negative charge : -395.3595 centred at (gu) : 93.11029 89.38857 93.73557 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 158338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24728 grid for indexing accessible points = 1.400000 m= 74264 mr = 111163 m= 24597 mr = 58195 m= 5167 mr = 18520 m= 606 mr = 3385 m= 36 mr = 304 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 3468 time to turn everything in is 0.8700000 number of dielectric boundary points 71438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19878 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) : 1.816574 object centre at (A) : -0.6359997 35.77250 22.21750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8035128E-02 -8.7268271E-02 midg,1,midg; midg,igrid,midg 0.2497121 -0.2803576 1,midg,midg; igrid,midg,midg 0.1777727 0.1327132 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.110000 now iterating at: 19:35:29 rms-change max change #iterations 9.537954 290.9153 at 10iterations 5.582341 151.2842 at 20iterations 3.231639 97.57024 at 30iterations 1.865935 46.72615 at 40iterations 1.072119 24.60363 at 50iterations 0.6153675 13.76398 at 60iterations 0.3519143 7.606539 at 70iterations 0.2011902 4.580283 at 80iterations 0.1148473 2.266416 at 90iterations 6.5560758E-02 1.288078 at 100iterations 3.7309911E-02 0.7690210 at 110iterations 2.1272605E-02 0.4309425 at 120iterations 1.2109793E-02 0.2425671 at 130iterations 6.8961498E-03 0.1273994 at 140iterations 3.9303480E-03 7.0513844E-02 at 150iterations 2.2358992E-03 4.3060303E-02 at 160iterations 1.2729305E-03 2.7290344E-02 at 170iterations 7.2355417E-04 1.5575647E-02 at 180iterations finished qdiffx linear iterations at : 19:35:40 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 7.2355417E-04 1.5575647E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 19:35:40 12.443u 0.210s 0:13.00 97.3% 0+0k 0+0io 0pf+0w