Sat Oct 8 11:44:07 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 11:44:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 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: 0.6366579 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): -24.93600 30.98100 ymin,ymax (A): -5.760000 40.42300 zmin,zma (A): 7.843000 55.43400 x,y,z range (A): 55.91700 46.18300 47.59100 scale (grids/A): 0.6366579 object centre (A): 3.022499 17.33150 31.63850 number of atom coordinates read : 2543 total number of charged atoms : 2403 net assigned charge : -1.999997 assigned positive charge : 387.8611 centred at (gu) : 90.00213 89.36482 89.55136 assigned negative charge : -389.8616 centred at (gu) : 90.13428 89.25446 89.63247 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6768 nv = 96 ne = 84 npr = 51994 no. pairs analyzed = 51994 no. exposed pairs = 3037 no. arc points = 22099 no. surface atoms = 1025 nbur = 1518 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3687 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2000000 number of dielectric boundary points 3399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2167 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8198 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6523640E-09 -1.0284083E-08 midg,1,midg; midg,igrid,midg -1.6684924E-08 7.8846325E-09 1,midg,midg; igrid,midg,midg 1.1340422E-08 -1.6926110E-08 gauss-seidel spectral radius is 0.9872124 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 11:44:08 rms-change max change #iterations 0.1398566 19.94160 at 10iterations 1.3853667E-02 2.001630 at 20iterations 1.3389514E-03 0.1654243 at 30iterations 1.3109535E-04 2.0117760E-02 at 40iterations 1.2738631E-05 2.1133423E-03 at 50iterations finished qdiffx linear iterations at : 11:44:11 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.2738631E-05 2.1133423E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 11:44:11 3.508u 0.185s 0:04.22 87.2% 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 11:44:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 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: 1.909974 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): -24.93600 30.98100 ymin,ymax (A): -5.760000 40.42300 zmin,zma (A): 7.843000 55.43400 x,y,z range (A): 55.91700 46.18300 47.59100 scale (grids/A): 1.909974 object centre (A): 3.022499 17.33150 31.63850 number of atom coordinates read : 2543 total number of charged atoms : 2403 net assigned charge : -1.999997 assigned positive charge : 387.8611 centred at (gu) : 90.00616 88.09413 88.65363 assigned negative charge : -389.8616 centred at (gu) : 90.40267 87.76329 88.89731 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22099 grid for indexing accessible points = 1.400000 m= 25329 mr = 50516 m= 4134 mr = 18469 m= 286 mr = 2642 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2190 time to turn everything in is 0.3700000 number of dielectric boundary points 31324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18889 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) : 0.6366579 object centre at (A) : 3.022499 17.33150 31.63850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0722417E-02 -2.6678022E-02 midg,1,midg; midg,igrid,midg -1.2257197E-02 3.0796271E-04 1,midg,midg; igrid,midg,midg 2.4432492E-02 -5.1947527E-02 gauss-seidel spectral radius is 0.9986368 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 11:44:12 rms-change max change #iterations 4.256769 173.1731 at 10iterations 1.991108 71.93636 at 20iterations 0.9347355 31.09756 at 30iterations 0.4371374 13.60797 at 40iterations 0.2048905 6.693849 at 50iterations 9.6298411E-02 2.921253 at 60iterations 4.4945449E-02 1.481628 at 70iterations 2.1096833E-02 0.6647358 at 80iterations 9.9057909E-03 0.3085852 at 90iterations 4.6306732E-03 0.1437950 at 100iterations 2.1637774E-03 7.6283455E-02 at 110iterations 1.0160903E-03 3.1609058E-02 at 120iterations finished qdiffx linear iterations at : 11:44:19 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.0160903E-03 3.1609058E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 11:44:20 8.032u 0.209s 0:08.54 96.3% 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 Sat Oct 8 2011 at 11:44:20 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 = 2543 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: 2.864961 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): -24.93600 30.98100 ymin,ymax (A): -5.760000 40.42300 zmin,zma (A): 7.843000 55.43400 x,y,z range (A): 55.91700 46.18300 47.59100 scale (grids/A): 2.864961 object centre (A): 3.022499 17.33150 31.63850 number of atom coordinates read : 2543 total number of charged atoms : 2403 net assigned charge : -1.999997 assigned positive charge : 387.8611 centred at (gu) : 90.00897 87.14115 87.98028 assigned negative charge : -389.8616 centred at (gu) : 90.60394 86.64484 88.34584 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 169393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22099 grid for indexing accessible points = 1.400000 m= 83044 mr = 122455 m= 29461 mr = 67549 m= 7465 mr = 23630 m= 1272 mr = 5666 m= 86 mr = 932 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 7799 time to turn everything in is 0.9400000 number of dielectric boundary points 70455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19223 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) : 1.909974 object centre at (A) : 3.022499 17.33150 31.63850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2521754 -0.4116713 midg,1,midg; midg,igrid,midg -0.1121857 -4.3970440E-02 1,midg,midg; igrid,midg,midg 0.3187177 -0.6921985 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 1.180000 now iterating at: 11:44:21 rms-change max change #iterations 9.833597 362.3739 at 10iterations 5.710346 116.6562 at 20iterations 3.283345 67.69203 at 30iterations 1.888353 36.94017 at 40iterations 1.086330 21.31406 at 50iterations 0.6222537 11.54897 at 60iterations 0.3571755 6.519862 at 70iterations 0.2047960 3.748507 at 80iterations 0.1174798 2.162855 at 90iterations 6.7291260E-02 1.263552 at 100iterations 3.8559213E-02 0.7330551 at 110iterations 2.2054277E-02 0.4318886 at 120iterations 1.2661115E-02 0.2544082 at 130iterations 7.2625363E-03 0.1412220 at 140iterations 4.1563907E-03 7.4884415E-02 at 150iterations 2.3852845E-03 4.3009758E-02 at 160iterations 1.3693402E-03 2.3672104E-02 at 170iterations 7.8277354E-04 1.5079379E-02 at 180iterations finished qdiffx linear iterations at : 11:44:33 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 7.8277354E-04 1.5079379E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 11:44:33 13.060u 0.212s 0:13.56 97.8% 0+0k 0+0io 0pf+0w