Sat Oct 8 14:26:55 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 Sat Oct 8 2011 at 14:26:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 500 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: 0.6383933 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): -35.85900 14.10700 ymin,ymax (A): -15.60600 35.80200 zmin,zma (A): -45.05600 10.70900 x,y,z range (A): 49.96600 51.40800 55.76500 scale (grids/A): 0.6383933 object centre (A): -10.87600 10.09800 -17.17350 number of atom coordinates read : 3036 total number of charged atoms : 2889 net assigned charge : 8.1211329E-06 assigned positive charge : 454.7755 centred at (gu) : 88.43641 89.04029 87.43916 assigned negative charge : -454.7763 centred at (gu) : 88.38822 88.99185 87.53463 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7980 nv = 96 ne = 84 npr = 64837 no. pairs analyzed = 64837 no. exposed pairs = 3433 no. arc points = 23684 no. surface atoms = 1174 nbur = 1862 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 4634 m= 2 mr = 32 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 3701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2383 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1289715E-08 -7.2857218E-09 midg,1,midg; midg,igrid,midg -7.9904803E-09 4.9224482E-09 1,midg,midg; igrid,midg,midg -9.0917798E-09 4.2994919E-09 gauss-seidel spectral radius is 0.9873148 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 14:26:56 rms-change max change #iterations 0.1622454 21.32469 at 10iterations 1.6436502E-02 2.261433 at 20iterations 1.6968428E-03 0.2010803 at 30iterations 1.8399228E-04 2.4097443E-02 at 40iterations 2.3823866E-05 3.1738281E-03 at 50iterations finished qdiffx linear iterations at : 14:26:59 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.3823866E-05 3.1738281E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:26:59 3.332u 0.170s 0:03.78 92.5% 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 14:26:59 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 500 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: 1.915180 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): -35.85900 14.10700 ymin,ymax (A): -15.60600 35.80200 zmin,zma (A): -45.05600 10.70900 x,y,z range (A): 49.96600 51.40800 55.76500 scale (grids/A): 1.915180 object centre (A): -10.87600 10.09800 -17.17350 number of atom coordinates read : 3036 total number of charged atoms : 2889 net assigned charge : 8.1211329E-06 assigned positive charge : 454.7755 centred at (gu) : 85.30830 87.12022 82.31668 assigned negative charge : -454.7763 centred at (gu) : 85.16429 86.97534 82.60382 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23684 grid for indexing accessible points = 1.400000 m= 30404 mr = 63464 m= 4298 mr = 22517 m= 216 mr = 2528 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 0.6200000 number of dielectric boundary points 34000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22776 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) : 0.6383933 object centre at (A) : -10.87600 10.09800 -17.17350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4609716E-02 -2.9226393E-02 midg,1,midg; midg,igrid,midg -7.4391798E-03 1.1954120E-02 1,midg,midg; igrid,midg,midg -8.1559997E-03 6.1357236E-03 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.9000000 now iterating at: 14:27:00 rms-change max change #iterations 4.741040 178.6568 at 10iterations 2.248060 66.20574 at 20iterations 1.067238 32.35735 at 30iterations 0.5079221 14.68949 at 40iterations 0.2408159 7.583447 at 50iterations 0.1142686 3.200231 at 60iterations 5.4319076E-02 1.941795 at 70iterations 2.5794357E-02 0.7924125 at 80iterations 1.2223556E-02 0.4086170 at 90iterations 5.8208550E-03 0.1713314 at 100iterations 2.7638709E-03 8.6629868E-02 at 110iterations 1.3158233E-03 3.7263870E-02 at 120iterations finished qdiffx linear iterations at : 14:27:10 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.3158233E-03 3.7263870E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:27:11 7.734u 0.209s 0:11.50 68.9% 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 14:27:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: NAP 500 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: 2.872770 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): -35.85900 14.10700 ymin,ymax (A): -15.60600 35.80200 zmin,zma (A): -45.05600 10.70900 x,y,z range (A): 49.96600 51.40800 55.76500 scale (grids/A): 2.872770 object centre (A): -10.87600 10.09800 -17.17350 number of atom coordinates read : 3036 total number of charged atoms : 2889 net assigned charge : 8.1211329E-06 assigned positive charge : 454.7755 centred at (gu) : 82.96227 85.68019 78.47484 assigned negative charge : -454.7763 centred at (gu) : 82.74635 85.46302 78.90566 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 203570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23684 grid for indexing accessible points = 1.400000 m= 101324 mr = 153610 m= 34285 mr = 83910 m= 7379 mr = 27406 m= 922 mr = 5321 m= 38 mr = 554 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 877 time to turn everything in is 1.480000 number of dielectric boundary points 76710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 23112 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) : 1.915180 object centre at (A) : -10.87600 10.09800 -17.17350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7076592 -0.2827948 midg,1,midg; midg,igrid,midg 2.9953539E-02 9.5412865E-02 1,midg,midg; igrid,midg,midg -4.1314267E-02 4.9861684E-02 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 1.760000 now iterating at: 14:27:13 rms-change max change #iterations 10.89388 363.8113 at 10iterations 6.376329 126.4396 at 20iterations 3.714886 69.59517 at 30iterations 2.162018 48.49599 at 40iterations 1.254542 21.28140 at 50iterations 0.7281345 13.18640 at 60iterations 0.4214082 7.339022 at 70iterations 0.2437705 4.380995 at 80iterations 0.1412715 2.438190 at 90iterations 8.1753641E-02 1.289785 at 100iterations 4.7233276E-02 0.7768800 at 110iterations 2.7301621E-02 0.4484701 at 120iterations 1.5804235E-02 0.2589035 at 130iterations 9.1450820E-03 0.1507301 at 140iterations 5.2909995E-03 8.9477539E-02 at 150iterations 3.0725803E-03 5.5886269E-02 at 160iterations 1.7846836E-03 3.0300140E-02 at 170iterations 1.0420335E-03 1.6654968E-02 at 180iterations finished qdiffx linear iterations at : 14:27:22 total time elapsed so far: 11.27000 # loops : 180 mean,max change (kT/e) : 1.0420335E-03 1.6654968E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 14:27:23 11.443u 0.184s 0:11.91 97.5% 0+0k 0+0io 0pf+0w