Sun Oct 9 02:56:57 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 Sun Oct 9 2011 at 02:56:57 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4364564 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 0.4364564 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 652.3193 centred at (gu) : 85.92264 91.13662 88.87314 assigned negative charge : -631.3239 centred at (gu) : 85.90577 91.10017 88.89487 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5094 nv = 96 ne = 84 npr = 90506 no. pairs analyzed = 90506 no. exposed pairs = 5666 no. arc points = 39639 no. surface atoms = 1942 nbur = 2520 mkacc time = 0.2500000 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 = 1.932000 m= 132 mr = 2405 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 2820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3257 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 6876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0228338E-11 3.5348716E-12 midg,1,midg; midg,igrid,midg 2.9534977E-12 1.1391154E-11 1,midg,midg; igrid,midg,midg 1.7778759E-11 2.1358867E-12 gauss-seidel spectral radius is 0.9732140 estimated iterations to convergence 51 setup time was (sec) 0.7600000 now iterating at: 02:56:58 rms-change max change #iterations 2.8387716E-02 5.508159 at 10iterations 2.7032322E-03 0.5186386 at 20iterations 7.4481807E-04 0.1507568 at 30iterations 2.1711127E-04 4.4404984E-02 at 40iterations 6.3411979E-05 1.3015747E-02 at 50iterations finished qdiffx linear iterations at : 02:57:02 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 6.3411979E-05 1.3015747E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 02:57:02 4.494u 0.334s 0:05.14 93.7% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 02:57:02 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.309369 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 1.309369 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 652.3193 centred at (gu) : 77.76624 93.40832 86.61787 assigned negative charge : -631.3239 centred at (gu) : 77.71692 93.30000 86.68449 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 59188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39639 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 13714 mr = 38918 m= 690 mr = 8097 m= 6 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.6000000 number of dielectric boundary points 26428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 730 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 29707 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) : 0.4364564 object centre at (A) : 37.35800 33.23050 196.7875 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3305699E-03 6.8565091E-04 midg,1,midg; midg,igrid,midg 1.6640681E-03 2.8074486E-03 1,midg,midg; igrid,midg,midg 2.3475630E-02 3.3312007E-03 gauss-seidel spectral radius is 0.9972546 estimated iterations to convergence 152 setup time was (sec) 0.9000000 now iterating at: 02:57:04 rms-change max change #iterations 2.396590 114.7770 at 10iterations 0.8198828 41.30920 at 20iterations 0.2810522 11.80542 at 30iterations 9.6286982E-02 4.115435 at 40iterations 3.3343494E-02 1.447079 at 50iterations 1.1721962E-02 0.4577365 at 60iterations 4.4431807E-03 0.2092686 at 70iterations 1.9826125E-03 8.8552475E-02 at 80iterations 1.0802775E-03 4.8095703E-02 at 90iterations 6.7632203E-04 2.9005051E-02 at 100iterations 4.4614592E-04 1.8995285E-02 at 110iterations 2.9813653E-04 1.2660980E-02 at 120iterations finished qdiffx linear iterations at : 02:57:12 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.9813653E-04 1.2660980E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 02:57:13 9.644u 0.354s 0:10.36 96.4% 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 Sun Oct 9 2011 at 02:57:13 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4462 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.964054 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): -3.425000 78.14100 ymin,ymax (A): 1.107000 65.35400 zmin,zma (A): 166.5010 227.0740 x,y,z range (A): 81.56600 64.24699 60.57298 scale (grids/A): 1.964054 object centre (A): 37.35800 33.23050 196.7875 number of atom coordinates read : 4462 total number of charged atoms : 4231 net assigned charge : 21.00000 assigned positive charge : 652.3193 centred at (gu) : 71.64894 95.11192 84.92642 assigned negative charge : -631.3239 centred at (gu) : 71.57533 94.94992 85.02654 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 139028 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39639 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 53260 mr = 97300 m= 9766 mr = 39267 m= 717 mr = 6160 m= 15 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1526 time to turn everything in is 1.370000 number of dielectric boundary points 59773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 33451 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) : 1.309369 object centre at (A) : 37.35800 33.23050 196.7875 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8233326E-02 1.4702967E-02 midg,1,midg; midg,igrid,midg 3.7984874E-02 3.2790415E-02 1,midg,midg; igrid,midg,midg 0.5615904 3.7511542E-02 gauss-seidel spectral radius is 0.9988520 estimated iterations to convergence 234 setup time was (sec) 1.700000 now iterating at: 02:57:15 rms-change max change #iterations 7.209784 229.0728 at 10iterations 3.722198 116.8365 at 20iterations 1.909253 56.13828 at 30iterations 0.9764512 31.69833 at 40iterations 0.4953468 12.35553 at 50iterations 0.2515373 7.318316 at 60iterations 0.1273174 3.278613 at 70iterations 6.4109914E-02 1.550759 at 80iterations 3.2351814E-02 0.8543320 at 90iterations 1.6335053E-02 0.4053917 at 100iterations 8.2320888E-03 0.2112064 at 110iterations 4.1797496E-03 0.1078472 at 120iterations 2.1552425E-03 5.4233074E-02 at 130iterations 1.1400346E-03 3.4492493E-02 at 140iterations 6.3097960E-04 1.5609741E-02 at 150iterations 3.7954230E-04 1.0192871E-02 at 160iterations 2.4875844E-04 7.2669983E-03 at 170iterations 1.7436084E-04 4.3525696E-03 at 180iterations finished qdiffx linear iterations at : 02:57:29 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 1.7436084E-04 4.3525696E-03 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 02:57:29 15.789u 0.364s 0:16.40 98.4% 0+0k 0+0io 0pf+0w