Mon Oct 10 09:25:47 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 09:25:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.5990039 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 0.5990039 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 286.9561 centred at (gu) : 89.83098 89.15485 90.52612 assigned negative charge : -281.9563 centred at (gu) : 89.81039 89.05657 90.65052 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4689 nv = 96 ne = 84 npr = 40453 no. pairs analyzed = 40453 no. exposed pairs = 2516 no. arc points = 17609 no. surface atoms = 854 nbur = 1104 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 = 1.456000 m= 211 mr = 2493 m= 2 mr = 19 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 0.2600000 number of dielectric boundary points 2390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1840 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6778856E-09 -1.2824486E-09 midg,1,midg; midg,igrid,midg -5.5279165E-10 3.8154204E-09 1,midg,midg; igrid,midg,midg 1.6490986E-09 2.5495452E-09 gauss-seidel spectral radius is 0.9855219 estimated iterations to convergence 68 setup time was (sec) 0.4700000 now iterating at: 09:25:47 rms-change max change #iterations 9.1823041E-02 14.80347 at 10iterations 7.6133069E-03 1.365528 at 20iterations 6.4303220E-04 0.1058197 at 30iterations 5.3554086E-05 9.1183186E-03 at 40iterations 4.5829702E-06 8.0871582E-04 at 50iterations finished qdiffx linear iterations at : 09:25:50 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 4.5829702E-06 8.0871582E-04 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 09:25:50 3.029u 0.142s 0:03.45 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 Mon Oct 10 2011 at 09:25:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.797012 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 1.797012 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 286.9561 centred at (gu) : 89.49281 87.46457 91.57850 assigned negative charge : -281.9563 centred at (gu) : 89.43112 87.16997 91.95155 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 51083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17609 grid for indexing accessible points = 1.400000 m= 16806 mr = 34551 m= 1959 mr = 12163 m= 97 mr = 1120 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 22087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14266 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) : 0.5990039 object centre at (A) : 20.98400 29.50300 17.27850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0545393E-02 -6.4235722E-04 midg,1,midg; midg,igrid,midg 1.1654861E-03 5.4384707E-03 1,midg,midg; igrid,midg,midg 3.6533348E-02 3.1897329E-02 gauss-seidel spectral radius is 0.9983917 estimated iterations to convergence 198 setup time was (sec) 0.6300000 now iterating at: 09:25:51 rms-change max change #iterations 3.149797 180.1858 at 10iterations 1.385420 55.35088 at 20iterations 0.6076448 23.21779 at 30iterations 0.2662442 10.91378 at 40iterations 0.1161613 4.435359 at 50iterations 5.1005818E-02 2.032171 at 60iterations 2.2456545E-02 0.8492064 at 70iterations 9.8588476E-03 0.3775215 at 80iterations 4.3259324E-03 0.1855073 at 90iterations 1.8847305E-03 7.0008636E-02 at 100iterations 8.3192979E-04 3.0167580E-02 at 110iterations 3.6497891E-04 1.6801834E-02 at 120iterations finished qdiffx linear iterations at : 09:25:57 total time elapsed so far: 6.410000 # loops : 120 mean,max change (kT/e) : 3.6497891E-04 1.6801834E-02 energy calculations done at 6.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.580000 DelPhi exited at 09:25:57 6.581u 0.170s 0:07.11 94.9% 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 09:25:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.695518 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 2.695518 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 286.9561 centred at (gu) : 89.23919 86.19684 92.36772 assigned negative charge : -281.9563 centred at (gu) : 89.14680 85.75512 92.92737 start vw surface at 0.1300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 118026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17609 grid for indexing accessible points = 1.400000 m= 56271 mr = 83701 m= 17586 mr = 45564 m= 3126 mr = 13974 m= 377 mr = 2201 m= 16 mr = 216 m= 0 mr = 5 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 49741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14605 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) : 1.797012 object centre at (A) : 20.98400 29.50300 17.27850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1006741 1.6310764E-02 midg,1,midg; midg,igrid,midg 4.2243674E-02 4.1823771E-02 1,midg,midg; igrid,midg,midg 0.4516371 0.3274297 gauss-seidel spectral radius is 0.9991730 estimated iterations to convergence 275 setup time was (sec) 1.130000 now iterating at: 09:25:59 rms-change max change #iterations 7.698318 298.0787 at 10iterations 4.380818 135.8611 at 20iterations 2.468491 59.99232 at 30iterations 1.382142 34.24488 at 40iterations 0.7746094 18.01719 at 50iterations 0.4316237 9.990873 at 60iterations 0.2403160 5.559593 at 70iterations 0.1339168 3.215203 at 80iterations 7.4489675E-02 1.885540 at 90iterations 4.1514128E-02 0.9185810 at 100iterations 2.3069561E-02 0.5253448 at 110iterations 1.2843697E-02 0.2833011 at 120iterations 7.1230424E-03 0.1556549 at 130iterations 3.9630369E-03 9.1037750E-02 at 140iterations 2.2024077E-03 4.7759533E-02 at 150iterations 1.2216445E-03 2.8037071E-02 at 160iterations 6.7777553E-04 1.6441345E-02 at 170iterations 3.7658389E-04 8.3541870E-03 at 180iterations finished qdiffx linear iterations at : 09:26:08 total time elapsed so far: 10.04000 # loops : 180 mean,max change (kT/e) : 3.7658389E-04 8.3541870E-03 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.22000 DelPhi exited at 09:26:08 10.222u 0.147s 0:10.64 97.3% 0+0k 0+0io 0pf+0w