Sat Oct 15 13:00:40 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 Sat Oct 15 2011 at 13:00:41 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.7044483 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): -6.625000 43.91100 ymin,ymax (A): -13.96800 36.18300 zmin,zma (A): 1.985000 45.04100 x,y,z range (A): 50.53600 50.15100 43.05600 scale (grids/A): 0.7044483 object centre (A): 18.64300 11.10750 23.51300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406019 assigned positive charge : 362.4292 centred at (gu) : 89.62174 91.33551 90.74438 assigned negative charge : -359.0236 centred at (gu) : 89.65047 91.50076 90.79498 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7916 nv = 96 ne = 84 npr = 47477 no. pairs analyzed = 47477 no. exposed pairs = 2939 no. arc points = 20683 no. surface atoms = 996 nbur = 1370 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4399 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7597965E-08 1.2150356E-09 midg,1,midg; midg,igrid,midg 8.8151850E-08 -8.0355122E-08 1,midg,midg; igrid,midg,midg 4.6773380E-08 1.2149642E-08 gauss-seidel spectral radius is 0.9895273 estimated iterations to convergence 80 setup time was (sec) 0.4200000 now iterating at: 13:00:41 rms-change max change #iterations 0.2153289 32.38020 at 10iterations 2.6603781E-02 3.323124 at 20iterations 3.7962422E-03 0.5766754 at 30iterations 7.5430755E-04 0.1142883 at 40iterations 2.1029935E-04 3.3538818E-02 at 50iterations finished qdiffx linear iterations at : 13:00:45 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 2.1029935E-04 3.3538818E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 13:00:45 4.043u 0.271s 0:04.71 91.5% 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 Sat Oct 15 2011 at 13:00:45 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.113345 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): -6.625000 43.91100 ymin,ymax (A): -13.96800 36.18300 zmin,zma (A): 1.985000 45.04100 x,y,z range (A): 50.53600 50.15100 43.05600 scale (grids/A): 2.113345 object centre (A): 18.64300 11.10750 23.51300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406019 assigned positive charge : 362.4292 centred at (gu) : 88.86465 94.00616 92.23277 assigned negative charge : -359.0236 centred at (gu) : 88.95116 94.50219 92.38468 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 32400 mr = 58765 m= 5864 mr = 24182 m= 499 mr = 3826 m= 10 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 36106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 17659 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) : 0.7044483 object centre at (A) : 18.64300 11.10750 23.51300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3204566E-02 1.2404907E-02 midg,1,midg; midg,igrid,midg 1.9625479E-02 -5.8319509E-02 1,midg,midg; igrid,midg,midg 5.8641180E-02 -1.7981021E-02 gauss-seidel spectral radius is 0.9988561 estimated iterations to convergence 234 setup time was (sec) 0.7200000 now iterating at: 13:00:46 rms-change max change #iterations 5.001865 233.3276 at 10iterations 2.489419 85.61542 at 20iterations 1.240741 40.92251 at 30iterations 0.6198900 20.12431 at 40iterations 0.3096199 9.412601 at 50iterations 0.1547325 4.224921 at 60iterations 7.7627897E-02 2.415147 at 70iterations 3.8884487E-02 1.182090 at 80iterations 1.9644979E-02 0.5918655 at 90iterations 9.9609774E-03 0.2769699 at 100iterations 5.1332177E-03 0.1505318 at 110iterations 2.7206300E-03 8.6280823E-02 at 120iterations finished qdiffx linear iterations at : 13:00:55 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 2.7206300E-03 8.6280823E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 13:00:55 9.355u 0.304s 0:10.11 95.4% 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 Sat Oct 15 2011 at 13:00:55 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.170017 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): -6.625000 43.91100 ymin,ymax (A): -13.96800 36.18300 zmin,zma (A): 1.985000 45.04100 x,y,z range (A): 50.53600 50.15100 43.05600 scale (grids/A): 3.170017 object centre (A): 18.64300 11.10750 23.51300 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406019 assigned positive charge : 362.4292 centred at (gu) : 88.29697 96.00913 93.34902 assigned negative charge : -359.0236 centred at (gu) : 88.42680 96.75330 93.57698 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 194293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 102146 mr = 141402 m= 39763 mr = 84405 m= 10738 mr = 32288 m= 2146 mr = 8164 m= 269 mr = 1582 m= 6 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 81340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17764 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) : 2.113345 object centre at (A) : 18.64300 11.10750 23.51300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4708190 -4.4180965E-03 midg,1,midg; midg,igrid,midg 0.4389227 -0.6422229 1,midg,midg; igrid,midg,midg 0.5694741 -0.5033919 gauss-seidel spectral radius is 0.9993061 estimated iterations to convergence 299 setup time was (sec) 1.690000 now iterating at: 13:00:57 rms-change max change #iterations 11.16792 388.4465 at 10iterations 6.651939 143.1094 at 20iterations 3.949340 77.06508 at 30iterations 2.338462 45.80978 at 40iterations 1.381876 24.41724 at 50iterations 0.8162323 12.93774 at 60iterations 0.4809976 9.129085 at 70iterations 0.2836426 4.845593 at 80iterations 0.1671152 2.685534 at 90iterations 9.8304249E-02 1.728104 at 100iterations 5.7939727E-02 0.9877510 at 110iterations 3.4440354E-02 0.5568771 at 120iterations 2.0595796E-02 0.3658295 at 130iterations 1.2548283E-02 0.2342072 at 140iterations 7.9140840E-03 0.1533661 at 150iterations 5.2208817E-03 0.1066704 at 160iterations 3.6512739E-03 7.5054169E-02 at 170iterations 2.7214047E-03 5.9059143E-02 at 180iterations finished qdiffx linear iterations at : 13:01:12 total time elapsed so far: 15.80000 # loops : 180 mean,max change (kT/e) : 2.7214047E-03 5.9059143E-02 energy calculations done at 15.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 13:01:12 15.944u 0.309s 0:16.53 98.2% 0+0k 0+0io 0pf+0w