Sun Oct 9 18:43:27 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 Sun Oct 9 2011 at 18:43:27 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5257 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5495948 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): 3.220000 67.99500 ymin,ymax (A): -8.948000 54.32000 zmin,zma (A): -1.028000 61.39900 x,y,z range (A): 64.77500 63.26800 62.42700 scale (grids/A): 0.5495948 object centre (A): 35.60750 22.68600 30.18550 number of atom coordinates read : 5257 total number of charged atoms : 5115 net assigned charge : -0.3789439 assigned positive charge : 808.1902 centred at (gu) : 88.10471 88.93439 89.46752 assigned negative charge : -808.5754 centred at (gu) : 87.96426 88.96612 89.41283 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10233 nv = 96 ne = 84 npr = 107233 no. pairs analyzed = 107233 no. exposed pairs = 6063 no. arc points = 41601 no. surface atoms = 2067 nbur = 3190 mkacc time = 0.2800000 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 = 1.540000 m= 433 mr = 5824 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4233 ## 507 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 13576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4735552E-10 6.6594125E-10 midg,1,midg; midg,igrid,midg 5.8735022E-10 -3.2451972E-10 1,midg,midg; igrid,midg,midg -3.1487273E-09 1.1949403E-09 gauss-seidel spectral radius is 0.9830908 estimated iterations to convergence 63 setup time was (sec) 0.9100000 now iterating at: 18:43:28 rms-change max change #iterations 0.1058701 15.54055 at 10iterations 1.0080186E-02 1.317486 at 20iterations 3.0771017E-03 0.3397369 at 30iterations 1.4180989E-03 0.1660233 at 40iterations 6.7189551E-04 8.1285477E-02 at 50iterations finished qdiffx linear iterations at : 18:43:33 total time elapsed so far: 5.500000 # loops : 50 mean,max change (kT/e) : 6.7189551E-04 8.1285477E-02 energy calculations done at 5.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 18:43:33 5.681u 0.459s 0:06.46 94.8% 0+0k 0+0io 6pf+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 18:43:33 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5257 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.648784 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): 3.220000 67.99500 ymin,ymax (A): -8.948000 54.32000 zmin,zma (A): -1.028000 61.39900 x,y,z range (A): 64.77500 63.26800 62.42700 scale (grids/A): 1.648784 object centre (A): 35.60750 22.68600 30.18550 number of atom coordinates read : 5257 total number of charged atoms : 5115 net assigned charge : -0.3789439 assigned positive charge : 808.1902 centred at (gu) : 84.31269 86.80190 88.40098 assigned negative charge : -808.5754 centred at (gu) : 83.89225 86.89829 88.23833 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 114772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39193 mr = 83397 m= 4617 mr = 28285 m= 146 mr = 2450 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 0.9900000 number of dielectric boundary points 44573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 400 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 39221 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) : 0.5495948 object centre at (A) : 35.60750 22.68600 30.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7286971E-02 -7.1478663E-03 midg,1,midg; midg,igrid,midg 1.8251197E-02 5.0028549E-03 1,midg,midg; igrid,midg,midg -2.8471731E-02 1.5792156E-02 gauss-seidel spectral radius is 0.9984223 estimated iterations to convergence 200 setup time was (sec) 1.360000 now iterating at: 18:43:35 rms-change max change #iterations 4.850320 198.7089 at 10iterations 2.150629 65.63239 at 20iterations 0.9548101 26.81489 at 30iterations 0.4242162 11.84726 at 40iterations 0.1883290 4.862175 at 50iterations 8.3942585E-02 2.556477 at 60iterations 3.7596676E-02 1.007038 at 70iterations 1.7238664E-02 0.4609795 at 80iterations 8.2543492E-03 0.2531509 at 90iterations 4.3639122E-03 0.1274910 at 100iterations 2.6333646E-03 7.8826904E-02 at 110iterations 1.7927265E-03 4.3601990E-02 at 120iterations finished qdiffx linear iterations at : 18:43:48 total time elapsed so far: 14.06000 # loops : 120 mean,max change (kT/e) : 1.7927265E-03 4.3601990E-02 energy calculations done at 14.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.24000 DelPhi exited at 18:43:48 14.248u 0.519s 0:15.05 98.0% 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 18:43:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5257 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.473176 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): 3.220000 67.99500 ymin,ymax (A): -8.948000 54.32000 zmin,zma (A): -1.028000 61.39900 x,y,z range (A): 64.77500 63.26800 62.42700 scale (grids/A): 2.473176 object centre (A): 35.60750 22.68600 30.18550 number of atom coordinates read : 5257 total number of charged atoms : 5115 net assigned charge : -0.3789439 assigned positive charge : 808.1902 centred at (gu) : 81.46862 85.20226 87.60108 assigned negative charge : -808.5754 centred at (gu) : 80.83830 85.34746 87.35734 start vw surface at 0.1800000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 267486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41601 grid for indexing accessible points = 1.400000 m= 133225 mr = 203401 m= 41505 mr = 108815 m= 7509 mr = 32249 m= 594 mr = 5041 m= 6 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 1.580000 no. cavity mid-points inaccessible to solvent = 918 time to turn everything in is 2.480000 number of dielectric boundary points 100517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.660000 number of grid points assigned charge 40884 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) : 1.648784 object centre at (A) : 35.60750 22.68600 30.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4256995 -0.2458264 midg,1,midg; midg,igrid,midg 0.1350947 -3.2801409E-03 1,midg,midg; igrid,midg,midg -0.5039235 0.1724811 gauss-seidel spectral radius is 0.9992518 estimated iterations to convergence 289 setup time was (sec) 2.910000 now iterating at: 18:43:52 rms-change max change #iterations 12.33784 356.6722 at 10iterations 7.278720 142.3860 at 20iterations 4.268370 90.70819 at 30iterations 2.490798 46.76093 at 40iterations 1.443195 27.26751 at 50iterations 0.8380322 15.59750 at 60iterations 0.4840066 8.269093 at 70iterations 0.2796862 4.823661 at 80iterations 0.1615869 2.509859 at 90iterations 9.3179390E-02 1.510521 at 100iterations 5.3835019E-02 0.8976746 at 110iterations 3.1237543E-02 0.5415840 at 120iterations 1.8323740E-02 0.3232651 at 130iterations 1.0958333E-02 0.1965485 at 140iterations 6.7884345E-03 0.1182442 at 150iterations 4.4322503E-03 7.6812744E-02 at 160iterations 3.1033806E-03 5.5681229E-02 at 170iterations 2.3276361E-03 3.9801598E-02 at 180iterations finished qdiffx linear iterations at : 18:44:13 total time elapsed so far: 24.20000 # loops : 180 mean,max change (kT/e) : 2.3276361E-03 3.9801598E-02 energy calculations done at 24.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.37000 DelPhi exited at 18:44:14 24.373u 0.555s 0:25.19 98.9% 0+0k 0+0io 0pf+0w