Mon Oct 10 19:34:00 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 19:34:00 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5785608 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 0.5785608 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 384.2927 centred at (gu) : 88.42393 90.40154 88.97942 assigned negative charge : -366.6935 centred at (gu) : 88.53517 90.40902 89.06214 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5654 nv = 96 ne = 84 npr = 50198 no. pairs analyzed = 50198 no. exposed pairs = 3382 no. arc points = 24414 no. surface atoms = 1128 nbur = 1410 mkacc time = 0.1300000 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 = 1.512000 m= 246 mr = 2801 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2800000 number of dielectric boundary points 3085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2514 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3451799E-09 1.7243504E-09 midg,1,midg; midg,igrid,midg 3.3996788E-09 3.7969041E-09 1,midg,midg; igrid,midg,midg 7.9292404E-09 1.1827100E-09 gauss-seidel spectral radius is 0.9845506 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 19:34:01 rms-change max change #iterations 9.0095386E-02 13.58008 at 10iterations 7.0191501E-03 1.187389 at 20iterations 5.5079529E-04 9.3067169E-02 at 30iterations 4.9464714E-05 8.1119537E-03 at 40iterations 5.6562722E-06 1.1577606E-03 at 50iterations finished qdiffx linear iterations at : 19:34:04 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 5.6562722E-06 1.1577606E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 19:34:05 3.971u 0.434s 0:04.79 91.8% 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 19:34:05 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.735682 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 1.735682 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 384.2927 centred at (gu) : 85.27127 91.20403 86.93753 assigned negative charge : -366.6935 centred at (gu) : 85.60519 91.22678 87.18636 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24414 grid for indexing accessible points = 1.400000 m= 19314 mr = 40950 m= 2164 mr = 12978 m= 83 mr = 1117 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 596 time to turn everything in is 0.5000000 number of dielectric boundary points 28655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18628 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) : 0.5785608 object centre at (A) : -0.2290010 32.48050 67.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6003412E-02 2.2275832E-02 midg,1,midg; midg,igrid,midg 1.1692462E-02 1.9561240E-02 1,midg,midg; igrid,midg,midg 3.0221974E-02 1.1775051E-02 gauss-seidel spectral radius is 0.9983557 estimated iterations to convergence 196 setup time was (sec) 0.7800000 now iterating at: 19:34:06 rms-change max change #iterations 3.455637 177.2609 at 10iterations 1.489953 62.52899 at 20iterations 0.6453940 23.36878 at 30iterations 0.2799842 10.55454 at 40iterations 0.1222262 4.921159 at 50iterations 5.2813385E-02 1.917648 at 60iterations 2.2817817E-02 0.7531347 at 70iterations 9.9876961E-03 0.4020019 at 80iterations 4.3251240E-03 0.1557636 at 90iterations 1.8833389E-03 7.3942184E-02 at 100iterations 8.1657642E-04 3.6483765E-02 at 110iterations 3.5812796E-04 1.4297485E-02 at 120iterations finished qdiffx linear iterations at : 19:34:14 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 3.5812796E-04 1.4297485E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 19:34:15 9.391u 0.466s 0:10.24 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 19:34:15 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.603523 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 2.603523 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 384.2927 centred at (gu) : 82.90672 91.80580 85.40623 assigned negative charge : -366.6935 centred at (gu) : 83.40773 91.84007 85.77951 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 143967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24414 grid for indexing accessible points = 1.400000 m= 66109 mr = 100332 m= 19558 mr = 51470 m= 3570 mr = 14474 m= 380 mr = 2386 m= 10 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 1948 time to turn everything in is 1.230000 number of dielectric boundary points 64740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19187 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) : 1.735682 object centre at (A) : -0.2290010 32.48050 67.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5959687 0.3123356 midg,1,midg; midg,igrid,midg 0.1544275 0.3150041 1,midg,midg; igrid,midg,midg 0.1717156 5.9084319E-02 gauss-seidel spectral radius is 0.9991805 estimated iterations to convergence 276 setup time was (sec) 1.540000 now iterating at: 19:34:17 rms-change max change #iterations 8.689295 270.1370 at 10iterations 4.980271 157.3043 at 20iterations 2.827169 69.74841 at 30iterations 1.596816 36.26403 at 40iterations 0.8989626 19.68089 at 50iterations 0.5051894 10.82855 at 60iterations 0.2828056 6.053802 at 70iterations 0.1581869 4.057571 at 80iterations 8.8426188E-02 1.841422 at 90iterations 4.9313530E-02 1.015242 at 100iterations 2.7560120E-02 0.5532799 at 110iterations 1.5388724E-02 0.3279791 at 120iterations 8.5613960E-03 0.1717033 at 130iterations 4.7880965E-03 9.4306946E-02 at 140iterations 2.6683246E-03 5.2707672E-02 at 150iterations 1.4888607E-03 3.1329155E-02 at 160iterations 8.3140068E-04 1.5871048E-02 at 170iterations 4.6364867E-04 9.3574524E-03 at 180iterations finished qdiffx linear iterations at : 19:34:31 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 4.6364867E-04 9.3574524E-03 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 19:34:32 15.730u 0.494s 0:16.69 97.1% 0+0k 0+0io 0pf+0w