Sat Oct 8 20:28:46 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 20:28:46 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 = 2570 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: 0.6344567 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 0.6344567 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.57590 89.15832 89.78420 assigned negative charge : -386.5045 centred at (gu) : 88.46904 89.21129 89.67161 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 53396 no. pairs analyzed = 53396 no. exposed pairs = 3008 no. arc points = 21441 no. surface atoms = 1010 nbur = 1560 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3735 m= 0 mr = 46 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3800000 number of dielectric boundary points 3283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2090 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1935915E-09 1.4840806E-08 midg,1,midg; midg,igrid,midg 1.1664768E-08 -6.3721217E-10 1,midg,midg; igrid,midg,midg -8.6975680E-09 1.1045366E-08 gauss-seidel spectral radius is 0.9871237 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 20:28:47 rms-change max change #iterations 0.1401293 20.60833 at 10iterations 1.3652578E-02 1.872597 at 20iterations 1.3558068E-03 0.2005424 at 30iterations 1.4619141E-04 2.1266937E-02 at 40iterations 2.0685102E-05 3.8461685E-03 at 50iterations finished qdiffx linear iterations at : 20:28:50 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 2.0685102E-05 3.8461685E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 20:28:51 4.496u 0.429s 0:05.18 94.7% 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 20:28:51 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 = 2570 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: 1.903370 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 1.903370 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 85.72707 87.47449 89.35248 assigned negative charge : -386.5045 centred at (gu) : 85.40690 87.63354 89.01457 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 grid for indexing accessible points = 1.400000 m= 25819 mr = 51164 m= 3851 mr = 19002 m= 207 mr = 2386 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3361 time to turn everything in is 0.7400000 number of dielectric boundary points 30344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19270 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) : 0.6344567 object centre at (A) : -7.157001 -0.2054996 16.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9047365E-02 2.6010005E-02 midg,1,midg; midg,igrid,midg 1.4711824E-02 -2.1552251E-04 1,midg,midg; igrid,midg,midg -7.5268704E-03 3.4978986E-02 gauss-seidel spectral radius is 0.9986280 estimated iterations to convergence 214 setup time was (sec) 1.070000 now iterating at: 20:28:52 rms-change max change #iterations 4.207810 170.8972 at 10iterations 1.965708 61.54353 at 20iterations 0.9199910 30.48387 at 30iterations 0.4296019 14.99933 at 40iterations 0.2001826 6.139179 at 50iterations 9.3779400E-02 2.885739 at 60iterations 4.3968525E-02 1.561760 at 70iterations 2.0509180E-02 0.6494274 at 80iterations 9.6107693E-03 0.3168809 at 90iterations 4.4850693E-03 0.1413412 at 100iterations 2.0990870E-03 6.5177917E-02 at 110iterations 9.8746957E-04 3.3058167E-02 at 120iterations finished qdiffx linear iterations at : 20:29:01 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 9.8746957E-04 3.3058167E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 20:29:02 10.266u 0.454s 0:11.04 97.0% 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 Sat Oct 8 2011 at 20:29:02 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 = 2570 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: 2.855055 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 2.855055 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 83.59058 86.21168 89.02866 assigned negative charge : -386.5045 centred at (gu) : 83.11021 86.45032 88.52180 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 169377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 grid for indexing accessible points = 1.400000 m= 84500 mr = 123593 m= 29060 mr = 69615 m= 6700 mr = 23277 m= 791 mr = 4999 m= 34 mr = 484 m= 0 mr = 14 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 11031 time to turn everything in is 1.910000 number of dielectric boundary points 68480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 19621 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) : 1.903370 object centre at (A) : -7.157001 -0.2054996 16.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7629786E-02 0.2847258 midg,1,midg; midg,igrid,midg 0.1720104 -3.5291888E-02 1,midg,midg; igrid,midg,midg -7.0773788E-02 0.4336674 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 2.270000 now iterating at: 20:29:05 rms-change max change #iterations 9.796381 381.8628 at 10iterations 5.665739 127.7299 at 20iterations 3.265876 66.03741 at 30iterations 1.877252 36.33289 at 40iterations 1.078415 20.24004 at 50iterations 0.6203706 11.98601 at 60iterations 0.3557328 6.484207 at 70iterations 0.2040222 3.940528 at 80iterations 0.1170084 2.321994 at 90iterations 6.6952087E-02 1.223770 at 100iterations 3.8356885E-02 0.6972675 at 110iterations 2.2054361E-02 0.3903562 at 120iterations 1.2583443E-02 0.2392616 at 130iterations 7.2140852E-03 0.1376171 at 140iterations 4.1344329E-03 7.8872681E-02 at 150iterations 2.3695612E-03 4.7376633E-02 at 160iterations 1.3609505E-03 2.6052475E-02 at 170iterations 7.7956548E-04 1.5081882E-02 at 180iterations finished qdiffx linear iterations at : 20:29:20 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 7.7956548E-04 1.5081882E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.90000 DelPhi exited at 20:29:21 17.909u 0.459s 0:18.64 98.4% 0+0k 0+0io 0pf+0w