Sat Oct 15 15:13:54 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 15:13:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6581867 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 0.6581867 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2721 net assigned charge : 1.162021 assigned positive charge : 433.1476 centred at (gu) : 90.96089 90.11242 90.86898 assigned negative charge : -431.9861 centred at (gu) : 90.78458 90.30254 90.77355 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8371 nv = 96 ne = 84 npr = 58792 no. pairs analyzed = 58792 no. exposed pairs = 3431 no. arc points = 24542 no. surface atoms = 1149 nbur = 1726 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4778 m= 5 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 91 time to turn everything in is 0.2200000 number of dielectric boundary points 4023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2332 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9835 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4861553E-08 2.6693087E-08 midg,1,midg; midg,igrid,midg 4.0508567E-08 -3.9333628E-08 1,midg,midg; igrid,midg,midg -2.8836759E-08 4.7491000E-08 gauss-seidel spectral radius is 0.9880606 estimated iterations to convergence 75 setup time was (sec) 0.4300000 now iterating at: 15:13:54 rms-change max change #iterations 0.1762788 28.27957 at 10iterations 1.8518079E-02 2.714783 at 20iterations 2.0178889E-03 0.2467785 at 30iterations 2.4838521E-04 3.3611298E-02 at 40iterations 4.8849153E-05 7.8163147E-03 at 50iterations finished qdiffx linear iterations at : 15:14:00 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 4.8849153E-05 7.8163147E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:14:01 3.592u 0.199s 0:07.21 52.4% 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 Sat Oct 15 2011 at 15:14:01 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.974560 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 1.974560 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2721 net assigned charge : 1.162021 assigned positive charge : 433.1476 centred at (gu) : 92.88210 90.33665 92.60617 assigned negative charge : -431.9861 centred at (gu) : 92.35323 90.90714 92.32030 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24542 grid for indexing accessible points = 1.400000 m= 35184 mr = 62603 m= 6219 mr = 26910 m= 383 mr = 4157 m= 9 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 0.4600000 number of dielectric boundary points 37097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 21484 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) : 0.6581867 object centre at (A) : 82.04350 32.65650 32.00200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0366237E-02 -3.2316092E-02 midg,1,midg; midg,igrid,midg 6.3078932E-02 -7.7357203E-02 1,midg,midg; igrid,midg,midg -1.0461098E-02 9.6842438E-02 gauss-seidel spectral radius is 0.9987555 estimated iterations to convergence 224 setup time was (sec) 0.7100000 now iterating at: 15:14:02 rms-change max change #iterations 4.840587 222.8706 at 10iterations 2.351728 75.96897 at 20iterations 1.137472 34.44567 at 30iterations 0.5539193 16.04292 at 40iterations 0.2690600 7.545008 at 50iterations 0.1305451 4.025496 at 60iterations 6.3319124E-02 1.907872 at 70iterations 3.0707866E-02 0.8703117 at 80iterations 1.4907531E-02 0.4523826 at 90iterations 7.2379499E-03 0.2009773 at 100iterations 3.5158091E-03 0.1097546 at 110iterations 1.7037377E-03 4.9183846E-02 at 120iterations finished qdiffx linear iterations at : 15:14:09 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 1.7037377E-03 4.9183846E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 15:14:10 8.527u 0.276s 0:09.10 96.5% 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 15:14:10 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.961840 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 2.961840 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2721 net assigned charge : 1.162021 assigned positive charge : 433.1476 centred at (gu) : 94.32291 90.50486 93.90928 assigned negative charge : -431.9861 centred at (gu) : 93.52975 91.36057 93.48023 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 205455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24542 grid for indexing accessible points = 1.400000 m= 110312 mr = 150664 m= 43972 mr = 92107 m= 11572 mr = 36523 m= 1755 mr = 9025 m= 136 mr = 1283 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 2856 time to turn everything in is 1.200000 number of dielectric boundary points 83551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21766 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) : 1.974560 object centre at (A) : 82.04350 32.65650 32.00200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4477565E-02 -1.026687 midg,1,midg; midg,igrid,midg 0.6479522 -1.155143 1,midg,midg; igrid,midg,midg 0.1921568 0.9323657 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 1.470000 now iterating at: 15:14:12 rms-change max change #iterations 11.03682 393.1570 at 10iterations 6.484643 142.4664 at 20iterations 3.807436 70.20572 at 30iterations 2.233454 38.77563 at 40iterations 1.306400 20.86246 at 50iterations 0.7642186 12.63513 at 60iterations 0.4474092 8.287281 at 70iterations 0.2612331 4.627328 at 80iterations 0.1525281 2.480993 at 90iterations 8.8851534E-02 1.477055 at 100iterations 5.1770352E-02 0.8952947 at 110iterations 3.0129829E-02 0.5037842 at 120iterations 1.7570322E-02 0.3087387 at 130iterations 1.0256853E-02 0.1762867 at 140iterations 5.9788697E-03 0.1010561 at 150iterations 3.4864077E-03 5.7170868E-02 at 160iterations 2.0328902E-03 3.5041809E-02 at 170iterations 1.1913819E-03 1.9941330E-02 at 180iterations finished qdiffx linear iterations at : 15:14:24 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 1.1913819E-03 1.9941330E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.10000 DelPhi exited at 15:14:25 14.105u 0.291s 0:14.70 97.8% 0+0k 0+0io 0pf+0w