Sat Oct 8 13:42:24 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 Sat Oct 8 2011 at 13:42:24 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3015 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6398504 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 0.6398504 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 1.4008060E-02 assigned positive charge : 452.4156 centred at (gu) : 88.81062 89.65465 91.93562 assigned negative charge : -452.4024 centred at (gu) : 88.78890 89.54660 91.88343 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8237 nv = 96 ne = 84 npr = 62891 no. pairs analyzed = 62891 no. exposed pairs = 3485 no. arc points = 23948 no. surface atoms = 1195 nbur = 1820 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 4806 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6721587E-09 1.0675973E-08 midg,1,midg; midg,igrid,midg -1.5908151E-08 1.3313067E-08 1,midg,midg; igrid,midg,midg -3.8424957E-09 2.2335713E-09 gauss-seidel spectral radius is 0.9873764 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 13:42:25 rms-change max change #iterations 0.1622833 22.11141 at 10iterations 1.6142517E-02 2.102921 at 20iterations 1.8559125E-03 0.3123550 at 30iterations 3.0276665E-04 4.0729523E-02 at 40iterations 6.9734531E-05 1.0311127E-02 at 50iterations finished qdiffx linear iterations at : 13:42:27 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 6.9734531E-05 1.0311127E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 13:42:28 3.187u 0.161s 0:03.63 92.0% 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 8 2011 at 13:42:28 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3015 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 1.919551 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 1.919551 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 1.4008060E-02 assigned positive charge : 452.4156 centred at (gu) : 86.43156 88.96331 95.80626 assigned negative charge : -452.4024 centred at (gu) : 86.36629 88.63949 95.64990 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23948 grid for indexing accessible points = 1.400000 m= 33622 mr = 64831 m= 5326 mr = 25458 m= 297 mr = 3372 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 35206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 22598 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) : 0.6398504 object centre at (A) : 15.78000 9.4995499E-03 19.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5121119E-02 1.2014528E-02 midg,1,midg; midg,igrid,midg -4.4996329E-03 1.7465077E-02 1,midg,midg; igrid,midg,midg -8.4868828E-03 2.2619249E-02 gauss-seidel spectral radius is 0.9986876 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 13:42:29 rms-change max change #iterations 4.716599 180.7590 at 10iterations 2.258798 69.57865 at 20iterations 1.073694 36.76562 at 30iterations 0.5120171 15.72618 at 40iterations 0.2433857 7.036839 at 50iterations 0.1161962 3.148488 at 60iterations 5.5382136E-02 1.695187 at 70iterations 2.6427079E-02 0.8076496 at 80iterations 1.2643539E-02 0.3704929 at 90iterations 6.0687745E-03 0.1845989 at 100iterations 2.9299646E-03 8.4098816E-02 at 110iterations 1.4229825E-03 4.2676926E-02 at 120iterations finished qdiffx linear iterations at : 13:42:35 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 1.4229825E-03 4.2676926E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 13:42:36 7.185u 0.236s 0:07.71 96.1% 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 8 2011 at 13:42:36 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3015 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.879327 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 2.879327 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 1.4008060E-02 assigned positive charge : 452.4156 centred at (gu) : 84.64723 88.44469 98.70934 assigned negative charge : -452.4024 centred at (gu) : 84.54935 87.95918 98.47482 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23948 grid for indexing accessible points = 1.400000 m= 108670 mr = 156762 m= 40203 mr = 90620 m= 9482 mr = 32665 m= 1302 mr = 7065 m= 59 mr = 850 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 79421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 22949 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) : 1.919551 object centre at (A) : 15.78000 9.4995499E-03 19.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1257487 0.2093301 midg,1,midg; midg,igrid,midg -1.2625657E-02 0.1908603 1,midg,midg; igrid,midg,midg 0.1271580 0.3420287 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.840000 now iterating at: 13:42:38 rms-change max change #iterations 11.01955 416.2626 at 10iterations 6.485321 163.2574 at 20iterations 3.798488 71.45353 at 30iterations 2.222777 38.73616 at 40iterations 1.292494 21.66007 at 50iterations 0.7526117 12.26401 at 60iterations 0.4374201 7.739462 at 70iterations 0.2538624 4.192024 at 80iterations 0.1477057 2.571603 at 90iterations 8.5578144E-02 1.425148 at 100iterations 4.9748939E-02 0.8756905 at 110iterations 2.8749531E-02 0.4543076 at 120iterations 1.6754726E-02 0.2953968 at 130iterations 9.7246347E-03 0.1625004 at 140iterations 5.6700520E-03 9.3850613E-02 at 150iterations 3.3219683E-03 5.6833267E-02 at 160iterations 1.9623991E-03 3.4105301E-02 at 170iterations 1.1746864E-03 1.9471169E-02 at 180iterations finished qdiffx linear iterations at : 13:42:47 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 1.1746864E-03 1.9471169E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 13:42:48 11.712u 0.253s 0:12.26 97.5% 0+0k 0+0io 0pf+0w