Mon Oct 10 18:36:37 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 18:36:38 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6621531 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 0.6621531 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000046 assigned positive charge : 323.7612 centred at (gu) : 92.31723 90.30312 90.99141 assigned negative charge : -323.2617 centred at (gu) : 92.26318 90.44037 91.11588 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6841 nv = 96 ne = 84 npr = 42865 no. pairs analyzed = 42865 no. exposed pairs = 2982 no. arc points = 21034 no. surface atoms = 996 nbur = 1199 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 3650 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1700000 number of dielectric boundary points 3601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7706 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8431811E-08 -2.5167701E-08 midg,1,midg; midg,igrid,midg 2.3300915E-08 -2.4135328E-08 1,midg,midg; igrid,midg,midg -4.8768811E-09 1.7610338E-08 gauss-seidel spectral radius is 0.9881549 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 18:36:38 rms-change max change #iterations 0.1523609 26.72888 at 10iterations 1.6465867E-02 2.568988 at 20iterations 1.7141844E-03 0.2485027 at 30iterations 1.9226175E-04 2.9026031E-02 at 40iterations 2.2984810E-05 3.5552979E-03 at 50iterations finished qdiffx linear iterations at : 18:36:41 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.2984810E-05 3.5552979E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 18:36:41 3.382u 0.186s 0:03.86 92.2% 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 Mon Oct 10 2011 at 18:36:41 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.986459 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 1.986459 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000046 assigned positive charge : 323.7612 centred at (gu) : 96.95119 90.90881 92.97378 assigned negative charge : -323.2617 centred at (gu) : 96.78944 91.32098 93.34754 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21034 grid for indexing accessible points = 1.400000 m= 29743 mr = 47771 m= 6274 mr = 22318 m= 481 mr = 4196 m= 4 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.3700000 number of dielectric boundary points 33240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16309 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) : 0.6621531 object centre at (A) : 7.459000 15.55300 23.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2745933E-02 8.5554952E-03 midg,1,midg; midg,igrid,midg 1.8771155E-02 -2.9057113E-03 1,midg,midg; igrid,midg,midg -8.0748098E-03 8.6721405E-03 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.5900000 now iterating at: 18:36:42 rms-change max change #iterations 4.168790 182.5507 at 10iterations 1.988818 72.51601 at 20iterations 0.9493820 29.13745 at 30iterations 0.4550531 14.48981 at 40iterations 0.2178909 6.834335 at 50iterations 0.1042529 3.360259 at 60iterations 5.0020926E-02 1.714802 at 70iterations 2.4035923E-02 0.7580795 at 80iterations 1.1489002E-02 0.3462262 at 90iterations 5.4923720E-03 0.1641951 at 100iterations 2.6421421E-03 8.3801270E-02 at 110iterations 1.2693023E-03 5.7098389E-02 at 120iterations finished qdiffx linear iterations at : 18:36:49 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.2693023E-03 5.7098389E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 18:36:50 7.854u 0.205s 0:08.37 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 Mon Oct 10 2011 at 18:36:50 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.979689 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 2.979689 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000046 assigned positive charge : 323.7612 centred at (gu) : 100.4267 91.36320 94.46043 assigned negative charge : -323.2617 centred at (gu) : 100.1841 91.98147 95.02129 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21034 grid for indexing accessible points = 1.400000 m= 88891 mr = 115517 m= 39666 mr = 72565 m= 11871 mr = 32681 m= 2107 mr = 9139 m= 145 mr = 1464 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 3362 time to turn everything in is 0.9800000 number of dielectric boundary points 74937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16472 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) : 1.986459 object centre at (A) : 7.459000 15.55300 23.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7550094 0.3107946 midg,1,midg; midg,igrid,midg 0.1609432 8.7506235E-02 1,midg,midg; igrid,midg,midg 3.5689462E-02 0.2090990 gauss-seidel spectral radius is 0.9992776 estimated iterations to convergence 294 setup time was (sec) 1.210000 now iterating at: 18:36:51 rms-change max change #iterations 9.687437 369.3080 at 10iterations 5.707567 135.3793 at 20iterations 3.342896 74.57948 at 30iterations 1.952428 44.81218 at 40iterations 1.137252 22.33051 at 50iterations 0.6602600 12.50243 at 60iterations 0.3830155 7.101713 at 70iterations 0.2222402 4.596448 at 80iterations 0.1291130 2.409237 at 90iterations 7.4739069E-02 1.381746 at 100iterations 4.3246035E-02 0.8997598 at 110iterations 2.5016589E-02 0.4317780 at 120iterations 1.4492873E-02 0.2679691 at 130iterations 8.3670272E-03 0.1593094 at 140iterations 4.8593185E-03 8.8700771E-02 at 150iterations 2.8033962E-03 5.3678513E-02 at 160iterations 1.6262855E-03 3.0587196E-02 at 170iterations 9.4091683E-04 1.8688202E-02 at 180iterations finished qdiffx linear iterations at : 18:37:03 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 9.4091683E-04 1.8688202E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 18:37:03 12.727u 0.217s 0:13.41 96.4% 0+0k 0+0io 0pf+0w