Mon Oct 10 14:12:21 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 Mon Oct 10 2011 at 14:12:22 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 = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 0.6502758 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 0.6502758 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 288.4070 centred at (gu) : 90.01648 92.10738 89.88879 assigned negative charge : -285.9253 centred at (gu) : 89.91780 92.24278 89.96760 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5773 nv = 96 ne = 84 npr = 40063 no. pairs analyzed = 40063 no. exposed pairs = 2565 no. arc points = 17783 no. surface atoms = 871 nbur = 1105 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3173 m= 0 mr = 55 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1741 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4308897E-08 -3.6746177E-09 midg,1,midg; midg,igrid,midg 1.2992278E-08 -1.6498676E-08 1,midg,midg; igrid,midg,midg -6.0283374E-09 1.6228810E-08 gauss-seidel spectral radius is 0.9876928 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 14:12:22 rms-change max change #iterations 0.1327082 20.56480 at 10iterations 1.3421654E-02 1.827361 at 20iterations 1.3931021E-03 0.1929321 at 30iterations 1.4371939E-04 2.3831844E-02 at 40iterations 1.4563335E-05 2.4307966E-03 at 50iterations finished qdiffx linear iterations at : 14:12:25 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.4563335E-05 2.4307966E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:12:25 3.072u 0.127s 0:03.57 89.3% 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 Mon Oct 10 2011 at 14:12:25 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 1.950827 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 1.950827 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 288.4070 centred at (gu) : 90.04928 96.32217 89.66635 assigned negative charge : -285.9253 centred at (gu) : 89.75370 96.72856 89.90299 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17783 grid for indexing accessible points = 1.400000 m= 23224 mr = 42449 m= 3897 mr = 17539 m= 245 mr = 2591 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 0.4700000 number of dielectric boundary points 26549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14504 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) : 0.6502758 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0875933E-03 4.7356252E-02 midg,1,midg; midg,igrid,midg 4.1109513E-02 -1.2763944E-02 1,midg,midg; igrid,midg,midg -5.2856607E-03 5.3507369E-03 gauss-seidel spectral radius is 0.9986272 estimated iterations to convergence 214 setup time was (sec) 0.7500000 now iterating at: 14:12:26 rms-change max change #iterations 3.721374 181.9546 at 10iterations 1.743051 69.57141 at 20iterations 0.8132572 30.83793 at 30iterations 0.3801313 15.34379 at 40iterations 0.1776407 6.043972 at 50iterations 8.2718097E-02 3.084370 at 60iterations 3.8643111E-02 1.368193 at 70iterations 1.8031372E-02 0.6083751 at 80iterations 8.4528523E-03 0.3215408 at 90iterations 3.9334963E-03 0.1257645 at 100iterations 1.8347392E-03 7.0657611E-02 at 110iterations 8.5965620E-04 2.9563904E-02 at 120iterations finished qdiffx linear iterations at : 14:12:32 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 8.5965620E-04 2.9563904E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 14:12:33 7.308u 0.197s 0:07.84 95.5% 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 Mon Oct 10 2011 at 14:12:33 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 = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.926241 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 2.926241 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 288.4070 centred at (gu) : 90.07404 99.48322 89.49947 assigned negative charge : -285.9253 centred at (gu) : 89.63061 100.0929 89.85464 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 142727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17783 grid for indexing accessible points = 1.400000 m= 73825 mr = 102548 m= 28330 mr = 60980 m= 7207 mr = 23376 m= 1137 mr = 5653 m= 78 mr = 805 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 1.180000 number of dielectric boundary points 59899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 14686 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) : 1.950827 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2525079E-02 0.8673378 midg,1,midg; midg,igrid,midg 0.4103846 -0.2003908 1,midg,midg; igrid,midg,midg -4.8186086E-02 1.6785378E-02 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.490000 now iterating at: 14:12:35 rms-change max change #iterations 8.716556 398.5439 at 10iterations 5.014026 121.8876 at 20iterations 2.871684 59.45747 at 30iterations 1.646401 32.34209 at 40iterations 0.9409616 18.42194 at 50iterations 0.5366963 11.49290 at 60iterations 0.3066676 5.809045 at 70iterations 0.1747463 3.877052 at 80iterations 9.9836074E-02 1.890039 at 90iterations 5.6999855E-02 1.173811 at 100iterations 3.2563884E-02 0.6583014 at 110iterations 1.8599313E-02 0.3528166 at 120iterations 1.0581397E-02 0.2018824 at 130iterations 6.0542747E-03 0.1310749 at 140iterations 3.4470821E-03 7.0541382E-02 at 150iterations 1.9661677E-03 3.6882162E-02 at 160iterations 1.1261149E-03 2.2613525E-02 at 170iterations 6.4132514E-04 1.2680054E-02 at 180iterations finished qdiffx linear iterations at : 14:12:45 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 6.4132514E-04 1.2680054E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.84000 DelPhi exited at 14:12:46 11.846u 0.231s 0:12.72 94.8% 0+0k 0+0io 0pf+0w