Sat Oct 15 15:30:14 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 15 2011 at 15:30:14 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6897087 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 0.6897087 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1992 net assigned charge : 11.80001 assigned positive charge : 328.3539 centred at (gu) : 91.48611 89.76530 89.19810 assigned negative charge : -316.5541 centred at (gu) : 91.56260 89.70298 89.08228 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6736 nv = 96 ne = 84 npr = 43099 no. pairs analyzed = 43099 no. exposed pairs = 2534 no. arc points = 17250 no. surface atoms = 867 nbur = 1448 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 3896 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1687 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0414753E-08 8.8566850E-08 midg,1,midg; midg,igrid,midg 4.6581743E-08 8.2266396E-08 1,midg,midg; igrid,midg,midg 6.8034055E-08 5.2489060E-08 gauss-seidel spectral radius is 0.9890487 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 15:30:14 rms-change max change #iterations 0.1902665 25.85684 at 10iterations 2.2444246E-02 3.110514 at 20iterations 2.6209843E-03 0.3421955 at 30iterations 3.2188758E-04 4.1631699E-02 at 40iterations 4.4843146E-05 7.8735352E-03 at 50iterations finished qdiffx linear iterations at : 15:30:17 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.4843146E-05 7.8735352E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:30:17 3.337u 0.171s 0:03.91 89.5% 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 Sat Oct 15 2011 at 15:30:18 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.069126 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 2.069126 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1992 net assigned charge : 11.80001 assigned positive charge : 328.3539 centred at (gu) : 94.45819 89.29596 87.59414 assigned negative charge : -316.5541 centred at (gu) : 94.68795 89.10889 87.24694 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17250 grid for indexing accessible points = 1.400000 m= 28604 mr = 51225 m= 5371 mr = 21799 m= 438 mr = 3552 m= 7 mr = 215 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 0.3600000 number of dielectric boundary points 29521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15804 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) : 0.6897087 object centre at (A) : 39.29050 14.96700 45.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6594199E-02 5.9043653E-02 midg,1,midg; midg,igrid,midg 2.8674886E-02 4.7800515E-02 1,midg,midg; igrid,midg,midg 2.7266819E-02 4.0307887E-02 gauss-seidel spectral radius is 0.9987782 estimated iterations to convergence 227 setup time was (sec) 0.5600000 now iterating at: 15:30:18 rms-change max change #iterations 4.451120 179.3869 at 10iterations 2.187484 77.64075 at 20iterations 1.058905 33.74023 at 30iterations 0.5189754 18.29461 at 40iterations 0.2527060 7.845741 at 50iterations 0.1233121 3.524309 at 60iterations 6.0351778E-02 1.770368 at 70iterations 2.9517826E-02 0.8999052 at 80iterations 1.4416864E-02 0.4169617 at 90iterations 7.0630610E-03 0.2352672 at 100iterations 3.4408169E-03 0.1201744 at 110iterations 1.6893261E-03 6.0248375E-02 at 120iterations finished qdiffx linear iterations at : 15:30:25 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.6893261E-03 6.0248375E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 15:30:26 7.691u 0.220s 0:08.40 94.1% 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 15 2011 at 15:30:26 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.103689 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 3.103689 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1992 net assigned charge : 11.80001 assigned positive charge : 328.3539 centred at (gu) : 96.68717 88.94398 86.39111 assigned negative charge : -316.5541 centred at (gu) : 97.03186 88.66334 85.87042 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 165625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17250 grid for indexing accessible points = 1.400000 m= 89932 mr = 123170 m= 36066 mr = 74934 m= 10018 mr = 29757 m= 1864 mr = 7745 m= 160 mr = 1393 m= 3 mr = 82 m= 0 mr = 2 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1034 time to turn everything in is 1.090000 number of dielectric boundary points 66585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 15936 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) : 2.069126 object centre at (A) : 39.29050 14.96700 45.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4012486 0.4382991 midg,1,midg; midg,igrid,midg 0.2529560 0.4163452 1,midg,midg; igrid,midg,midg 0.2194492 0.5974525 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 15:30:27 rms-change max change #iterations 10.11977 416.7891 at 10iterations 5.943654 134.7929 at 20iterations 3.488657 78.50974 at 30iterations 2.044896 48.01640 at 40iterations 1.196193 24.42345 at 50iterations 0.6983550 12.19707 at 60iterations 0.4072190 7.913033 at 70iterations 0.2373403 4.401299 at 80iterations 0.1385972 2.568672 at 90iterations 8.0724992E-02 1.656815 at 100iterations 4.6968028E-02 0.9554291 at 110iterations 2.7318861E-02 0.5356140 at 120iterations 1.5859507E-02 0.2881165 at 130iterations 9.2369169E-03 0.1788521 at 140iterations 5.3864620E-03 9.8250389E-02 at 150iterations 3.1390169E-03 5.9839249E-02 at 160iterations 1.8310127E-03 3.1229019E-02 at 170iterations 1.0780921E-03 1.9947052E-02 at 180iterations finished qdiffx linear iterations at : 15:30:39 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 1.0780921E-03 1.9947052E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 15:30:39 12.597u 0.211s 0:13.07 97.9% 0+0k 0+0io 0pf+0w