Sat Oct 15 15:15:21 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 15 2011 at 15:15:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 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: 0.5549234 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 0.5549234 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3799 net assigned charge : 11.00002 assigned positive charge : 608.9774 centred at (gu) : 90.67476 90.30383 92.95033 assigned negative charge : -597.9813 centred at (gu) : 90.73675 90.26297 93.05140 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 76475 no. pairs analyzed = 76475 no. exposed pairs = 5477 no. arc points = 38829 no. surface atoms = 1797 nbur = 2161 mkacc time = 0.2600000 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 = 1.568000 m= 335 mr = 3806 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3990 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 10410 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1006239E-09 -6.0679828E-10 midg,1,midg; midg,igrid,midg 4.6504897E-10 1.6141369E-09 1,midg,midg; igrid,midg,midg 1.4928833E-09 2.6948221E-10 gauss-seidel spectral radius is 0.9833338 estimated iterations to convergence 64 setup time was (sec) 0.9200000 now iterating at: 15:15:22 rms-change max change #iterations 8.9711644E-02 12.80814 at 10iterations 6.2927427E-03 0.9394550 at 20iterations 5.0769455E-04 7.1807861E-02 at 30iterations 7.1518858E-05 9.6378326E-03 at 40iterations 1.9360825E-05 2.9506683E-03 at 50iterations finished qdiffx linear iterations at : 15:15:27 total time elapsed so far: 4.990000 # loops : 50 mean,max change (kT/e) : 1.9360825E-05 2.9506683E-03 energy calculations done at 4.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 15:15:28 5.224u 0.414s 0:06.50 86.6% 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 Sat Oct 15 2011 at 15:15:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 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: 1.664770 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 1.664770 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3799 net assigned charge : 11.00002 assigned positive charge : 608.9774 centred at (gu) : 92.02259 90.90961 98.84914 assigned negative charge : -597.9813 centred at (gu) : 92.20971 90.78835 99.15352 start vw surface at 0.2100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 87116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26827 mr = 56748 m= 2794 mr = 17387 m= 70 mr = 1206 m= 0 mr = 2 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 41464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 29173 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) : 0.5549234 object centre at (A) : 15.90750 55.56750 47.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8058628E-02 7.5345542E-03 midg,1,midg; midg,igrid,midg 1.7955983E-02 2.0981830E-02 1,midg,midg; igrid,midg,midg 3.5087239E-02 -4.7151502E-03 gauss-seidel spectral radius is 0.9983559 estimated iterations to convergence 196 setup time was (sec) 1.330000 now iterating at: 15:15:30 rms-change max change #iterations 4.080241 202.4824 at 10iterations 1.760062 71.05179 at 20iterations 0.7638791 25.02079 at 30iterations 0.3310035 10.91015 at 40iterations 0.1438269 5.237579 at 50iterations 6.2473938E-02 2.458238 at 60iterations 2.7123939E-02 0.8061619 at 70iterations 1.1754930E-02 0.3655300 at 80iterations 5.1382063E-03 0.1848130 at 90iterations 2.2356897E-03 7.5035095E-02 at 100iterations 9.7493979E-04 3.2904625E-02 at 110iterations 4.2625229E-04 1.3427734E-02 at 120iterations finished qdiffx linear iterations at : 15:15:51 total time elapsed so far: 12.67000 # loops : 120 mean,max change (kT/e) : 4.2625229E-04 1.3427734E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 15:15:52 12.897u 0.508s 0:24.26 55.1% 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 Sat Oct 15 2011 at 15:15:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 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: 2.497155 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): -15.69900 47.51400 ymin,ymax (A): 23.70900 87.42599 zmin,zma (A): 15.56300 79.71600 x,y,z range (A): 63.21300 63.71700 64.15300 scale (grids/A): 2.497155 object centre (A): 15.90750 55.56750 47.63950 number of atom coordinates read : 3958 total number of charged atoms : 3799 net assigned charge : 11.00002 assigned positive charge : 608.9774 centred at (gu) : 93.03357 91.36395 103.2731 assigned negative charge : -597.9813 centred at (gu) : 93.31448 91.18236 103.7301 start vw surface at 0.1900000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 202212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38829 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91726 mr = 139932 m= 26207 mr = 69832 m= 4209 mr = 18696 m= 285 mr = 2551 m= 4 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.290000 number of dielectric boundary points 93533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 30352 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) : 1.664770 object centre at (A) : 15.90750 55.56750 47.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1621238 8.3892412E-02 midg,1,midg; midg,igrid,midg 0.1769100 0.3442126 1,midg,midg; igrid,midg,midg 0.4895420 -7.9565883E-02 gauss-seidel spectral radius is 0.9992132 estimated iterations to convergence 281 setup time was (sec) 2.690000 now iterating at: 15:15:56 rms-change max change #iterations 10.62206 336.4290 at 10iterations 6.162648 141.1759 at 20iterations 3.551661 78.47900 at 30iterations 2.032430 41.97137 at 40iterations 1.162939 23.37265 at 50iterations 0.6629812 13.89993 at 60iterations 0.3771422 8.035856 at 70iterations 0.2144781 4.462334 at 80iterations 0.1215506 2.368962 at 90iterations 6.8819024E-02 1.273796 at 100iterations 3.8981222E-02 0.7123704 at 110iterations 2.2057097E-02 0.4182434 at 120iterations 1.2484289E-02 0.2209530 at 130iterations 7.0443107E-03 0.1320591 at 140iterations 3.9836583E-03 6.8963528E-02 at 150iterations 2.2564500E-03 4.4847488E-02 at 160iterations 1.2766384E-03 2.3817062E-02 at 170iterations 7.2444655E-04 1.2897491E-02 at 180iterations finished qdiffx linear iterations at : 15:16:31 total time elapsed so far: 21.55000 # loops : 180 mean,max change (kT/e) : 7.2444655E-04 1.2897491E-02 energy calculations done at 21.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.76000 DelPhi exited at 15:16:31 21.765u 0.597s 0:39.17 57.0% 0+0k 0+0io 0pf+0w