Mon Oct 10 13:59:05 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 13:59:05 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6304678 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 0.6304678 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.500007 assigned positive charge : 350.3655 centred at (gu) : 90.18451 89.96944 89.03912 assigned negative charge : -348.8660 centred at (gu) : 90.26546 89.86634 89.00047 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6456 nv = 96 ne = 84 npr = 43120 no. pairs analyzed = 43120 no. exposed pairs = 3491 no. arc points = 24713 no. surface atoms = 1155 nbur = 1170 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3069 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2354 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7741988E-09 3.9081667E-09 midg,1,midg; midg,igrid,midg -6.7317401E-09 9.8519903E-09 1,midg,midg; igrid,midg,midg 7.8475457E-09 -5.0720903E-09 gauss-seidel spectral radius is 0.9869608 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 13:59:06 rms-change max change #iterations 0.1297413 20.42621 at 10iterations 1.2148819E-02 1.699572 at 20iterations 1.1515602E-03 0.1774769 at 30iterations 1.1968359E-04 2.0293832E-02 at 40iterations 1.8846238E-05 3.7178993E-03 at 50iterations finished qdiffx linear iterations at : 13:59:09 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.8846238E-05 3.7178993E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 13:59:09 3.319u 0.173s 0:03.81 91.3% 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 13:59:09 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.891404 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 1.891404 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.500007 assigned positive charge : 350.3655 centred at (gu) : 90.55322 89.90822 87.11712 assigned negative charge : -348.8660 centred at (gu) : 90.79632 89.59907 87.00146 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24713 grid for indexing accessible points = 1.400000 m= 24613 mr = 43529 m= 4109 mr = 16731 m= 221 mr = 2287 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17100 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) : 0.6304678 object centre at (A) : 18.74950 15.53400 8.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6541426E-03 4.9313190E-03 midg,1,midg; midg,igrid,midg -2.9247662E-02 1.4557573E-02 1,midg,midg; igrid,midg,midg 1.6518747E-02 1.4720572E-03 gauss-seidel spectral radius is 0.9986159 estimated iterations to convergence 213 setup time was (sec) 0.8300000 now iterating at: 13:59:10 rms-change max change #iterations 3.983791 195.2620 at 10iterations 1.859190 67.60826 at 20iterations 0.8631821 32.70456 at 30iterations 0.4000614 14.74183 at 40iterations 0.1855406 6.823631 at 50iterations 8.6386010E-02 3.648890 at 60iterations 4.0180277E-02 1.266911 at 70iterations 1.8687187E-02 0.5882692 at 80iterations 8.6829755E-03 0.3063660 at 90iterations 4.0525808E-03 0.1351814 at 100iterations 1.8781631E-03 6.3721657E-02 at 110iterations 8.8056392E-04 2.9291153E-02 at 120iterations finished qdiffx linear iterations at : 13:59:17 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 8.8056392E-04 2.9291153E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 13:59:18 7.662u 0.158s 0:08.18 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 Mon Oct 10 2011 at 13:59:18 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 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: 2.837105 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 2.837105 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.500007 assigned positive charge : 350.3655 centred at (gu) : 90.82977 89.86230 85.67562 assigned negative charge : -348.8660 centred at (gu) : 91.19445 89.39857 85.50224 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 157505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24713 grid for indexing accessible points = 1.400000 m= 77229 mr = 106587 m= 29094 mr = 59724 m= 7311 mr = 22000 m= 949 mr = 5010 m= 52 mr = 513 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 78292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 17447 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) : 1.891404 object centre at (A) : 18.74950 15.53400 8.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7853575E-02 7.1552545E-02 midg,1,midg; midg,igrid,midg -0.1510674 0.3956961 1,midg,midg; igrid,midg,midg 0.2403751 -1.2823148E-02 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.640000 now iterating at: 13:59:20 rms-change max change #iterations 9.688638 409.5046 at 10iterations 5.812239 122.8086 at 20iterations 3.435700 73.54750 at 30iterations 2.022175 43.78686 at 40iterations 1.184281 26.78549 at 50iterations 0.6931156 14.77586 at 60iterations 0.4035370 7.984787 at 70iterations 0.2351131 4.488777 at 80iterations 0.1363104 2.728527 at 90iterations 7.9079524E-02 1.899592 at 100iterations 4.5803472E-02 0.9131546 at 110iterations 2.6500579E-02 0.5250874 at 120iterations 1.5321182E-02 0.2967415 at 130iterations 8.8989194E-03 0.1778691 at 140iterations 5.1354123E-03 0.1000910 at 150iterations 2.9717293E-03 5.8558464E-02 at 160iterations 1.7199914E-03 3.6869049E-02 at 170iterations 9.9782448E-04 1.7890811E-02 at 180iterations finished qdiffx linear iterations at : 13:59:30 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 9.9782448E-04 1.7890811E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 13:59:31 12.271u 0.205s 0:13.05 95.5% 0+0k 0+0io 0pf+0w