Sun Oct 9 15:42:47 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+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 Sun Oct 9 2011 at 15:42:48 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5331256 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 0.5331256 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4970 net assigned charge : 6.006029 assigned positive charge : 798.0671 centred at (gu) : 89.16188 89.06002 90.63764 assigned negative charge : -792.0677 centred at (gu) : 89.19585 88.98963 90.51984 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9118 nv = 96 ne = 84 npr = 103416 no. pairs analyzed = 103416 no. exposed pairs = 6184 no. arc points = 43282 no. surface atoms = 2086 nbur = 3052 mkacc time = 0.2200000 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 = 1.596000 m= 357 mr = 4910 m= 0 mr = 12 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4700000 number of dielectric boundary points 4553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4307 ## 607 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 12255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4501237E-10 1.2464165E-09 midg,1,midg; midg,igrid,midg -3.7645415E-10 5.7156452E-10 1,midg,midg; igrid,midg,midg 5.7467137E-10 -1.9140189E-11 gauss-seidel spectral radius is 0.9820206 estimated iterations to convergence 61 setup time was (sec) 0.6700000 now iterating at: 15:42:48 rms-change max change #iterations 8.8541314E-02 11.62341 at 10iterations 6.2417500E-03 0.8865280 at 20iterations 9.9798013E-04 0.1112556 at 30iterations 3.3056110E-04 4.5358181E-02 at 40iterations 1.1852286E-04 1.8308163E-02 at 50iterations finished qdiffx linear iterations at : 15:42:51 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.1852286E-04 1.8308163E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 15:42:51 3.286u 0.144s 0:03.78 90.4% 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 Sun Oct 9 2011 at 15:42:51 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.599377 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 1.599377 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4970 net assigned charge : 6.006029 assigned positive charge : 798.0671 centred at (gu) : 87.48389 87.17834 91.91090 assigned negative charge : -792.0677 centred at (gu) : 87.58710 86.96870 91.55938 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 102588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43282 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31499 mr = 71643 m= 3025 mr = 21866 m= 72 mr = 1466 m= 0 mr = 11 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2428 time to turn everything in is 0.6800000 number of dielectric boundary points 42198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 568 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 37829 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) : 0.5331256 object centre at (A) : 36.00050 91.71850 62.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2792247E-03 2.1142354E-02 midg,1,midg; midg,igrid,midg -3.9623365E-02 1.9788783E-02 1,midg,midg; igrid,midg,midg 5.5282512E-03 2.7315847E-03 gauss-seidel spectral radius is 0.9983091 estimated iterations to convergence 193 setup time was (sec) 0.9400000 now iterating at: 15:42:52 rms-change max change #iterations 4.430714 172.2524 at 10iterations 1.900780 61.76752 at 20iterations 0.8158335 25.43591 at 30iterations 0.3519138 11.08728 at 40iterations 0.1513138 4.437893 at 50iterations 6.5432876E-02 1.951742 at 60iterations 2.8152350E-02 0.8314812 at 70iterations 1.2266250E-02 0.3336840 at 80iterations 5.3470903E-03 0.1536446 at 90iterations 2.3883304E-03 8.1195831E-02 at 100iterations 1.1106104E-03 3.4478962E-02 at 110iterations 5.5377482E-04 1.6705513E-02 at 120iterations finished qdiffx linear iterations at : 15:42:59 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 5.5377482E-04 1.6705513E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 15:42:59 7.267u 0.173s 0:07.72 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 15:42:59 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.399065 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 2.399065 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4970 net assigned charge : 6.006029 assigned positive charge : 798.0671 centred at (gu) : 86.22552 85.76714 92.86561 assigned negative charge : -792.0677 centred at (gu) : 86.38067 85.45294 92.33900 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 239107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43282 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110090 mr = 175731 m= 30532 mr = 87688 m= 4623 mr = 22957 m= 291 mr = 2915 m= 3 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 7822 time to turn everything in is 1.640000 number of dielectric boundary points 95213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 39696 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) : 1.599377 object centre at (A) : 36.00050 91.71850 62.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5245301E-02 0.2896466 midg,1,midg; midg,igrid,midg -0.7836154 0.2093322 1,midg,midg; igrid,midg,midg 0.1126173 6.6163987E-02 gauss-seidel spectral radius is 0.9992254 estimated iterations to convergence 284 setup time was (sec) 1.930000 now iterating at: 15:43:01 rms-change max change #iterations 11.69008 340.0898 at 10iterations 6.844517 172.0882 at 20iterations 3.985120 91.79341 at 30iterations 2.303954 52.23729 at 40iterations 1.329877 26.53526 at 50iterations 0.7621968 14.24223 at 60iterations 0.4369209 8.193311 at 70iterations 0.2500479 4.605049 at 80iterations 0.1429100 2.603636 at 90iterations 8.1606783E-02 1.389306 at 100iterations 4.6642844E-02 0.8633919 at 110iterations 2.6511198E-02 0.4522018 at 120iterations 1.5089784E-02 0.3001881 at 130iterations 8.5951481E-03 0.1505947 at 140iterations 4.9015298E-03 8.4534168E-02 at 150iterations 2.7954441E-03 4.8904419E-02 at 160iterations 1.5961082E-03 2.6246727E-02 at 170iterations 9.1240957E-04 1.5388489E-02 at 180iterations finished qdiffx linear iterations at : 15:43:12 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 9.1240957E-04 1.5388489E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 15:43:12 12.446u 0.185s 0:12.92 97.6% 0+0k 0+0io 0pf+0w