Sun Oct 9 18:41:03 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 18:41:03 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2439 !!! WARNING: GLM 219 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6555083 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): 14.26500 66.99700 ymin,ymax (A): -5.561000 48.74800 zmin,zma (A): 21.87500 75.42300 x,y,z range (A): 52.73200 54.30900 53.54800 scale (grids/A): 0.6555083 object centre (A): 40.63100 21.59350 48.64900 number of atom coordinates read : 2439 total number of charged atoms : 2290 net assigned charge : -0.5939794 assigned positive charge : 358.6742 centred at (gu) : 89.99355 89.38086 88.40222 assigned negative charge : -359.2691 centred at (gu) : 89.96845 89.41640 88.32129 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7394 nv = 96 ne = 84 npr = 48080 no. pairs analyzed = 48080 no. exposed pairs = 3226 no. arc points = 23396 no. surface atoms = 1096 nbur = 1343 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 3965 m= 5 mr = 72 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8381 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0307182E-08 8.4828731E-09 midg,1,midg; midg,igrid,midg 5.2953237E-09 -6.0841385E-09 1,midg,midg; igrid,midg,midg -5.2288236E-09 2.9351346E-09 gauss-seidel spectral radius is 0.9879358 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 18:41:04 rms-change max change #iterations 0.1568462 21.81507 at 10iterations 1.6224766E-02 2.164619 at 20iterations 1.7079975E-03 0.2508373 at 30iterations 1.8046726E-04 2.7832031E-02 at 40iterations 1.8402201E-05 2.4075508E-03 at 50iterations finished qdiffx linear iterations at : 18:41:07 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.8402201E-05 2.4075508E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 18:41:07 3.141u 0.155s 0:03.59 91.6% 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 18:41:07 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2439 !!! WARNING: GLM 219 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.966525 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): 14.26500 66.99700 ymin,ymax (A): -5.561000 48.74800 zmin,zma (A): 21.87500 75.42300 x,y,z range (A): 52.73200 54.30900 53.54800 scale (grids/A): 1.966525 object centre (A): 40.63100 21.59350 48.64900 number of atom coordinates read : 2439 total number of charged atoms : 2290 net assigned charge : -0.5939794 assigned positive charge : 358.6742 centred at (gu) : 89.98041 88.14223 85.20599 assigned negative charge : -359.2691 centred at (gu) : 89.90555 88.24932 84.96393 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23396 grid for indexing accessible points = 1.400000 m= 30327 mr = 53285 m= 5702 mr = 22432 m= 419 mr = 3636 m= 8 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 401 time to turn everything in is 0.5500000 number of dielectric boundary points 35442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18104 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) : 0.6555083 object centre at (A) : 40.63100 21.59350 48.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1336209E-02 5.7800515E-03 midg,1,midg; midg,igrid,midg -4.5205881E-03 3.5347163E-03 1,midg,midg; igrid,midg,midg -4.1929325E-03 4.6607950E-03 gauss-seidel spectral radius is 0.9987127 estimated iterations to convergence 221 setup time was (sec) 0.8200000 now iterating at: 18:41:08 rms-change max change #iterations 4.332037 198.7493 at 10iterations 2.070012 65.87149 at 20iterations 0.9891012 30.21941 at 30iterations 0.4704449 14.97698 at 40iterations 0.2246633 6.848539 at 50iterations 0.1073619 3.651645 at 60iterations 5.1348031E-02 1.506352 at 70iterations 2.4444208E-02 0.7363381 at 80iterations 1.1715679E-02 0.3474731 at 90iterations 5.6182118E-03 0.1789436 at 100iterations 2.6811417E-03 8.5794449E-02 at 110iterations 1.2817576E-03 4.1961670E-02 at 120iterations finished qdiffx linear iterations at : 18:41:14 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.2817576E-03 4.1961670E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 18:41:15 7.036u 0.200s 0:07.50 96.4% 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 18:41:15 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2439 !!! WARNING: GLM 219 has a net charge of -0.0940 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: 2.949787 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): 14.26500 66.99700 ymin,ymax (A): -5.561000 48.74800 zmin,zma (A): 21.87500 75.42300 x,y,z range (A): 52.73200 54.30900 53.54800 scale (grids/A): 2.949787 object centre (A): 40.63100 21.59350 48.64900 number of atom coordinates read : 2439 total number of charged atoms : 2290 net assigned charge : -0.5939794 assigned positive charge : 358.6742 centred at (gu) : 89.97050 87.21341 82.80880 assigned negative charge : -359.2691 centred at (gu) : 89.85838 87.37404 82.44589 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 181079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23396 grid for indexing accessible points = 1.400000 m= 94723 mr = 129139 m= 37860 mr = 77204 m= 10437 mr = 30611 m= 1779 mr = 7860 m= 153 mr = 1185 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1364 time to turn everything in is 1.390000 number of dielectric boundary points 79961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 18320 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) : 1.966525 object centre at (A) : 40.63100 21.59350 48.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5189734 5.1138978E-03 midg,1,midg; midg,igrid,midg -0.1916256 3.8886782E-02 1,midg,midg; igrid,midg,midg -9.9238530E-02 9.9891536E-02 gauss-seidel spectral radius is 0.9992821 estimated iterations to convergence 294 setup time was (sec) 1.690000 now iterating at: 18:41:16 rms-change max change #iterations 10.15842 381.1161 at 10iterations 5.980481 125.5461 at 20iterations 3.516335 73.14213 at 30iterations 2.063043 41.12494 at 40iterations 1.200320 22.41049 at 50iterations 0.7002022 14.93094 at 60iterations 0.4063827 8.094578 at 70iterations 0.2358353 4.409736 at 80iterations 0.1373128 2.408674 at 90iterations 7.9529330E-02 1.431938 at 100iterations 4.6144571E-02 0.8820381 at 110iterations 2.6737683E-02 0.4440413 at 120iterations 1.5486217E-02 0.2725754 at 130iterations 8.9859525E-03 0.1727548 at 140iterations 5.1992498E-03 9.0881348E-02 at 150iterations 3.0216498E-03 5.1788330E-02 at 160iterations 1.7490550E-03 3.1684875E-02 at 170iterations 1.0150174E-03 1.6937256E-02 at 180iterations finished qdiffx linear iterations at : 18:41:26 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 1.0150174E-03 1.6937256E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 18:41:27 11.811u 0.221s 0:12.35 97.4% 0+0k 0+0io 0pf+0w