Tue Oct 11 06:01:17 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 Tue Oct 11 2011 at 06:01:17 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7071068 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 0.7071068 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1990 net assigned charge : 6.420009 assigned positive charge : 326.6560 centred at (gu) : 89.16496 90.14376 90.33762 assigned negative charge : -320.2360 centred at (gu) : 89.29781 90.08862 90.42538 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7158 nv = 96 ne = 84 npr = 42424 no. pairs analyzed = 42424 no. exposed pairs = 2600 no. arc points = 17585 no. surface atoms = 890 nbur = 1428 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4166 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1589 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7926 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0982830E-08 9.0733119E-09 midg,1,midg; midg,igrid,midg 2.4730980E-08 8.3178207E-08 1,midg,midg; igrid,midg,midg 1.4047167E-07 -1.1839966E-08 gauss-seidel spectral radius is 0.9895772 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 06:01:17 rms-change max change #iterations 0.2057468 31.16259 at 10iterations 2.5857134E-02 3.342846 at 20iterations 3.3526740E-03 0.4265062 at 30iterations 5.4767518E-04 7.0360184E-02 at 40iterations 1.4033551E-04 1.6572952E-02 at 50iterations finished qdiffx linear iterations at : 06:01:20 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.4033551E-04 1.6572952E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 06:01:21 3.505u 0.190s 0:04.04 91.3% 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 Tue Oct 11 2011 at 06:01:21 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.121320 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 2.121320 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1990 net assigned charge : 6.420009 assigned positive charge : 326.6560 centred at (gu) : 87.49509 90.43113 91.01322 assigned negative charge : -320.2360 centred at (gu) : 87.89329 90.26583 91.27608 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17585 grid for indexing accessible points = 1.400000 m= 31050 mr = 54191 m= 5967 mr = 23682 m= 537 mr = 4050 m= 21 mr = 277 m= 0 mr = 9 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 31412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15774 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) : 0.7071068 object centre at (A) : 48.89250 6.441000 25.06850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0382524E-02 2.6837453E-02 midg,1,midg; midg,igrid,midg 4.5171216E-02 2.7162939E-02 1,midg,midg; igrid,midg,midg 4.6863623E-02 -4.8494350E-02 gauss-seidel spectral radius is 0.9988323 estimated iterations to convergence 232 setup time was (sec) 0.6400000 now iterating at: 06:01:22 rms-change max change #iterations 4.704555 228.3676 at 10iterations 2.325805 77.71202 at 20iterations 1.156724 37.20016 at 30iterations 0.5739163 16.22623 at 40iterations 0.2851299 8.948929 at 50iterations 0.1412434 4.097354 at 60iterations 7.0304893E-02 2.006538 at 70iterations 3.5009705E-02 1.082174 at 80iterations 1.7467855E-02 0.5146562 at 90iterations 8.7397899E-03 0.2608624 at 100iterations 4.3819854E-03 0.1396933 at 110iterations 2.2370897E-03 6.2925339E-02 at 120iterations finished qdiffx linear iterations at : 06:01:29 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.2370897E-03 6.2925339E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 06:01:30 8.171u 0.216s 0:09.22 90.8% 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 Tue Oct 11 2011 at 06:01:30 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.181981 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): 25.70300 72.08200 ymin,ymax (A): -18.73200 31.61400 zmin,zma (A): 3.943000 46.19400 x,y,z range (A): 46.37900 50.34600 42.25100 scale (grids/A): 3.181981 object centre (A): 48.89250 6.441000 25.06850 number of atom coordinates read : 2318 total number of charged atoms : 1990 net assigned charge : 6.420009 assigned positive charge : 326.6560 centred at (gu) : 86.24267 90.64669 91.51976 assigned negative charge : -320.2360 centred at (gu) : 86.84010 90.39863 91.91412 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17585 grid for indexing accessible points = 1.400000 m= 96302 mr = 130320 m= 39466 mr = 80336 m= 11280 mr = 32620 m= 2186 mr = 8823 m= 322 mr = 1624 m= 17 mr = 213 m= 0 mr = 6 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15920 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) : 2.121320 object centre at (A) : 48.89250 6.441000 25.06850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1273363 0.2279856 midg,1,midg; midg,igrid,midg 0.3484030 0.1207377 1,midg,midg; igrid,midg,midg 0.4574463 -0.5978920 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.430000 now iterating at: 06:01:32 rms-change max change #iterations 10.50465 346.7543 at 10iterations 6.230852 137.4558 at 20iterations 3.691619 85.91078 at 30iterations 2.179654 54.32823 at 40iterations 1.285553 24.82499 at 50iterations 0.7570555 14.80939 at 60iterations 0.4443876 8.451550 at 70iterations 0.2615215 5.138760 at 80iterations 0.1534462 3.280693 at 90iterations 8.9969277E-02 1.754772 at 100iterations 5.2923225E-02 0.9028542 at 110iterations 3.1151392E-02 0.5479393 at 120iterations 1.8438000E-02 0.3232371 at 130iterations 1.0994618E-02 0.1969151 at 140iterations 6.6671981E-03 0.1328545 at 150iterations 4.1430746E-03 7.7713013E-02 at 160iterations 2.6891672E-03 6.3709259E-02 at 170iterations 1.8434398E-03 3.6117554E-02 at 180iterations finished qdiffx linear iterations at : 06:01:44 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.8434398E-03 3.6117554E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 06:01:44 13.582u 0.248s 0:14.37 96.1% 0+0k 0+0io 0pf+0w