Mon Oct 10 16:59:24 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 Mon Oct 10 2011 at 16:59:24 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: GLM 103 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5778471 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 0.5778471 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2719 net assigned charge : -9.3967229E-02 assigned positive charge : 427.3513 centred at (gu) : 89.56165 89.53470 89.72936 assigned negative charge : -427.4464 centred at (gu) : 89.54904 89.68349 89.82964 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6344 nv = 96 ne = 84 npr = 57647 no. pairs analyzed = 57647 no. exposed pairs = 3521 no. arc points = 25334 no. surface atoms = 1189 nbur = 1674 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 262 mr = 3348 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8112 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0462296E-09 -1.9092528E-09 midg,1,midg; midg,igrid,midg 3.1824330E-09 -2.7047187E-09 1,midg,midg; igrid,midg,midg -3.1636849E-10 1.9127547E-10 gauss-seidel spectral radius is 0.9845371 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 16:59:24 rms-change max change #iterations 9.7658969E-02 15.38123 at 10iterations 7.3642749E-03 1.151199 at 20iterations 5.7283771E-04 9.2712402E-02 at 30iterations 4.4752156E-05 8.7909698E-03 at 40iterations 3.7876252E-06 6.1988831E-04 at 50iterations finished qdiffx linear iterations at : 16:59:27 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.7876252E-06 6.1988831E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 16:59:28 3.444u 0.164s 0:04.20 85.7% 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 16:59:28 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: GLM 103 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.733541 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 1.733541 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2719 net assigned charge : -9.3967229E-02 assigned positive charge : 427.3513 centred at (gu) : 88.68423 88.60336 89.18709 assigned negative charge : -427.4464 centred at (gu) : 88.64680 89.05027 89.48850 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25334 grid for indexing accessible points = 1.400000 m= 22580 mr = 47591 m= 2615 mr = 16136 m= 93 mr = 1454 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2734 time to turn everything in is 0.3400000 number of dielectric boundary points 29847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21101 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) : 0.5778471 object centre at (A) : 14.52550 2.178000 44.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0504285E-03 -6.7834249E-03 midg,1,midg; midg,igrid,midg 6.8381475E-03 -1.9403894E-02 1,midg,midg; igrid,midg,midg -3.9391820E-03 -1.0981581E-02 gauss-seidel spectral radius is 0.9983873 estimated iterations to convergence 198 setup time was (sec) 0.5600000 now iterating at: 16:59:29 rms-change max change #iterations 3.723834 188.3488 at 10iterations 1.617586 56.65112 at 20iterations 0.7097478 24.32444 at 30iterations 0.3112833 11.95335 at 40iterations 0.1364950 4.817450 at 50iterations 5.9739422E-02 2.163330 at 60iterations 2.6185591E-02 0.9590716 at 70iterations 1.1464959E-02 0.3996887 at 80iterations 5.0202636E-03 0.1900043 at 90iterations 2.2087933E-03 8.9287758E-02 at 100iterations 9.6714788E-04 3.3790588E-02 at 110iterations 4.2396699E-04 1.3956070E-02 at 120iterations finished qdiffx linear iterations at : 16:59:36 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 4.2396699E-04 1.3956070E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 16:59:36 7.753u 0.220s 0:08.48 93.9% 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 16:59:37 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2863 !!! WARNING: GLM 103 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.600312 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 2.600312 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2719 net assigned charge : -9.3967229E-02 assigned positive charge : 427.3513 centred at (gu) : 88.02619 87.90493 88.78036 assigned negative charge : -427.4464 centred at (gu) : 87.97012 88.57536 89.23277 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25334 grid for indexing accessible points = 1.400000 m= 76640 mr = 116108 m= 23526 mr = 61754 m= 4331 mr = 18316 m= 342 mr = 3114 m= 6 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 8791 time to turn everything in is 0.8600000 number of dielectric boundary points 67323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21740 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) : 1.733541 object centre at (A) : 14.52550 2.178000 44.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1389208E-03 -6.6588067E-02 midg,1,midg; midg,igrid,midg 4.0797029E-02 -0.2289177 1,midg,midg; igrid,midg,midg -8.1813768E-02 -0.2107123 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.090000 now iterating at: 16:59:38 rms-change max change #iterations 9.175904 349.7665 at 10iterations 5.220888 144.1071 at 20iterations 2.953639 68.03235 at 30iterations 1.667539 39.76379 at 40iterations 0.9365033 24.39676 at 50iterations 0.5275325 11.68703 at 60iterations 0.2968845 7.306877 at 70iterations 0.1663994 3.261081 at 80iterations 9.3630269E-02 1.940889 at 90iterations 5.2575685E-02 1.039343 at 100iterations 2.9436335E-02 0.5521164 at 110iterations 1.6561341E-02 0.3865395 at 120iterations 9.2811892E-03 0.1911621 at 130iterations 5.1942822E-03 9.8165512E-02 at 140iterations 2.9160194E-03 6.1454773E-02 at 150iterations 1.6358623E-03 3.2814026E-02 at 160iterations 9.1542734E-04 2.0246506E-02 at 170iterations 5.1451480E-04 9.4461441E-03 at 180iterations finished qdiffx linear iterations at : 16:59:49 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 5.1451480E-04 9.4461441E-03 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 16:59:50 12.486u 0.218s 0:13.51 93.9% 0+0k 0+0io 0pf+0w