Sat Oct 8 14:27:25 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 Sat Oct 8 2011 at 14:27:25 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6109071 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 0.6109071 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 454.7356 centred at (gu) : 88.50211 89.05987 87.15070 assigned negative charge : -454.7223 centred at (gu) : 88.45216 89.01658 87.24965 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 64351 no. pairs analyzed = 64351 no. exposed pairs = 3427 no. arc points = 23973 no. surface atoms = 1173 nbur = 1858 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 4262 m= 0 mr = 19 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2445 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9284 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0938046E-08 -3.1623297E-09 midg,1,midg; midg,igrid,midg -3.2933138E-09 1.9695736E-09 1,midg,midg; igrid,midg,midg -4.3052379E-09 2.0151847E-09 gauss-seidel spectral radius is 0.9861558 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 14:27:26 rms-change max change #iterations 0.1296894 17.63988 at 10iterations 1.1790208E-02 1.719490 at 20iterations 1.2027606E-03 0.1773129 at 30iterations 1.5712679E-04 2.3139954E-02 at 40iterations 2.9636742E-05 4.9247742E-03 at 50iterations finished qdiffx linear iterations at : 14:27:31 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 2.9636742E-05 4.9247742E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 14:27:31 5.238u 0.481s 0:06.01 95.0% 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 14:27:31 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.832721 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 1.832721 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 454.7356 centred at (gu) : 85.50583 87.17915 81.45133 assigned negative charge : -454.7223 centred at (gu) : 85.35606 87.04951 81.74873 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 28157 mr = 58231 m= 3725 mr = 21001 m= 161 mr = 2205 m= 0 mr = 47 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 558 time to turn everything in is 0.6700000 number of dielectric boundary points 31520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22593 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) : 0.6109071 object centre at (A) : 1.996500 1.392500 6.315000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5837618E-02 -2.0983208E-02 midg,1,midg; midg,igrid,midg 1.6738395E-03 1.4083866E-02 1,midg,midg; igrid,midg,midg -8.9977561E-03 3.8845241E-03 gauss-seidel spectral radius is 0.9985586 estimated iterations to convergence 209 setup time was (sec) 1.010000 now iterating at: 14:27:33 rms-change max change #iterations 4.307396 174.0854 at 10iterations 1.980468 63.40126 at 20iterations 0.9109071 26.81707 at 30iterations 0.4190572 14.39153 at 40iterations 0.1925560 6.422688 at 50iterations 8.8564277E-02 2.794815 at 60iterations 4.0550228E-02 1.375095 at 70iterations 1.8700149E-02 0.5667582 at 80iterations 8.6230393E-03 0.2586060 at 90iterations 3.9643403E-03 0.1182364 at 100iterations 1.8235324E-03 5.6417465E-02 at 110iterations 8.4060477E-04 2.9739380E-02 at 120iterations finished qdiffx linear iterations at : 14:27:44 total time elapsed so far: 12.27000 # loops : 120 mean,max change (kT/e) : 8.4060477E-04 2.9739380E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 14:27:44 12.441u 0.552s 0:13.28 97.8% 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 Sat Oct 8 2011 at 14:27:44 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.749082 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 2.749082 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 454.7356 centred at (gu) : 83.25857 85.76840 77.17694 assigned negative charge : -454.7223 centred at (gu) : 83.03405 85.57407 77.62307 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 187703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 94141 mr = 140937 m= 31278 mr = 78136 m= 6331 mr = 25040 m= 690 mr = 4627 m= 16 mr = 386 m= 0 mr = 4 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1856 time to turn everything in is 1.740000 number of dielectric boundary points 71029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 23071 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) : 1.832721 object centre at (A) : 1.996500 1.392500 6.315000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6535194 -0.1646987 midg,1,midg; midg,igrid,midg 9.6592456E-02 0.1593130 1,midg,midg; igrid,midg,midg -5.3488217E-02 3.5857257E-02 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.130000 now iterating at: 14:27:47 rms-change max change #iterations 10.19320 267.8443 at 10iterations 5.902691 124.6574 at 20iterations 3.407997 68.69073 at 30iterations 1.955867 38.44167 at 40iterations 1.120409 23.05995 at 50iterations 0.6406370 11.45264 at 60iterations 0.3662834 6.857574 at 70iterations 0.2096990 3.793926 at 80iterations 0.1197991 2.068783 at 90iterations 6.8462186E-02 1.215742 at 100iterations 3.9115842E-02 0.6585052 at 110iterations 2.2292612E-02 0.3889694 at 120iterations 1.2749780E-02 0.2344904 at 130iterations 7.2802748E-03 0.1189747 at 140iterations 4.1563250E-03 6.8827391E-02 at 150iterations 2.3783068E-03 4.2818069E-02 at 160iterations 1.3588165E-03 2.4810791E-02 at 170iterations 7.7799207E-04 1.3442993E-02 at 180iterations finished qdiffx linear iterations at : 14:28:06 total time elapsed so far: 21.16000 # loops : 180 mean,max change (kT/e) : 7.7799207E-04 1.3442993E-02 energy calculations done at 21.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.34000 DelPhi exited at 14:28:07 21.340u 0.587s 0:22.16 98.9% 0+0k 0+0io 0pf+0w