Tue Oct 11 02:25:21 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 Tue Oct 11 2011 at 02:25:21 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: FMN 398 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6649110 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 0.6649110 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2595 net assigned charge : 5.500027 assigned positive charge : 420.7953 centred at (gu) : 90.76247 90.30804 90.20155 assigned negative charge : -415.2964 centred at (gu) : 90.57820 90.48283 90.25011 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8137 nv = 96 ne = 84 npr = 54974 no. pairs analyzed = 54974 no. exposed pairs = 3375 no. arc points = 23312 no. surface atoms = 1124 nbur = 1594 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4645 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3000000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2214 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9509 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6313476E-08 4.2582999E-09 midg,1,midg; midg,igrid,midg 5.3470863E-08 -2.8760402E-08 1,midg,midg; igrid,midg,midg -2.4788790E-08 6.9389110E-08 gauss-seidel spectral radius is 0.9882854 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 02:25:22 rms-change max change #iterations 0.1771370 24.73615 at 10iterations 2.0375781E-02 2.764065 at 20iterations 3.3617562E-03 0.5655670 at 30iterations 1.0424822E-03 0.2143135 at 40iterations 4.0027840E-04 8.3999634E-02 at 50iterations finished qdiffx linear iterations at : 02:25:24 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 4.0027840E-04 8.3999634E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 02:25:25 3.169u 0.185s 0:03.96 84.3% 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 Tue Oct 11 2011 at 02:25:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: FMN 398 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.994733 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 1.994733 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2595 net assigned charge : 5.500027 assigned positive charge : 420.7953 centred at (gu) : 92.28673 90.92336 90.60371 assigned negative charge : -415.2964 centred at (gu) : 91.73455 91.44846 90.75031 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 87084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23312 grid for indexing accessible points = 1.400000 m= 32597 mr = 61322 m= 5583 mr = 24484 m= 397 mr = 3595 m= 9 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1282 time to turn everything in is 0.6300000 number of dielectric boundary points 36106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20543 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) : 0.6649110 object centre at (A) : 43.75500 41.10350 6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6106693E-02 -2.9372154E-02 midg,1,midg; midg,igrid,midg 7.2719894E-02 -2.1495735E-02 1,midg,midg; igrid,midg,midg -1.8655799E-02 6.1668027E-02 gauss-seidel spectral radius is 0.9987631 estimated iterations to convergence 225 setup time was (sec) 0.9100000 now iterating at: 02:25:26 rms-change max change #iterations 4.870987 184.8615 at 10iterations 2.357114 82.75331 at 20iterations 1.145208 33.51059 at 30iterations 0.5559958 15.87761 at 40iterations 0.2714934 7.860325 at 50iterations 0.1314478 3.909575 at 60iterations 6.4135961E-02 1.974518 at 70iterations 3.1589232E-02 0.9891462 at 80iterations 1.5666567E-02 0.4817772 at 90iterations 8.0152350E-03 0.2729607 at 100iterations 4.2911633E-03 0.1711769 at 110iterations 2.4771367E-03 9.8579407E-02 at 120iterations finished qdiffx linear iterations at : 02:25:33 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.4771367E-03 9.8579407E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 02:25:34 7.566u 0.207s 0:08.43 92.0% 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 Tue Oct 11 2011 at 02:25:34 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: FMN 398 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: 2.992100 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 2.992100 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2595 net assigned charge : 5.500027 assigned positive charge : 420.7953 centred at (gu) : 93.42993 91.38493 90.90553 assigned negative charge : -415.2964 centred at (gu) : 92.60172 92.17263 91.12525 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 201138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23312 grid for indexing accessible points = 1.400000 m= 104270 mr = 148325 m= 39461 mr = 86105 m= 10290 mr = 32204 m= 1683 mr = 7861 m= 144 mr = 1177 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 4381 time to turn everything in is 1.530000 number of dielectric boundary points 81234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 20759 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) : 1.994733 object centre at (A) : 43.75500 41.10350 6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2144889 -0.3345653 midg,1,midg; midg,igrid,midg 0.9890612 -0.3429654 1,midg,midg; igrid,midg,midg -0.2086703 0.4816552 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 1.840000 now iterating at: 02:25:36 rms-change max change #iterations 11.20195 418.8974 at 10iterations 6.610920 154.2391 at 20iterations 3.894991 81.04676 at 30iterations 2.291775 39.47906 at 40iterations 1.346860 26.17165 at 50iterations 0.7899359 14.06850 at 60iterations 0.4617359 8.774788 at 70iterations 0.2702695 4.703729 at 80iterations 0.1580797 2.781544 at 90iterations 9.2331514E-02 1.663975 at 100iterations 5.4111484E-02 0.9441376 at 110iterations 3.1745162E-02 0.5403214 at 120iterations 1.8674817E-02 0.3809032 at 130iterations 1.1145577E-02 0.2222710 at 140iterations 6.8085021E-03 0.1378403 at 150iterations 4.3189055E-03 9.4429016E-02 at 160iterations 2.9116445E-03 6.8885803E-02 at 170iterations 2.0939554E-03 5.2215576E-02 at 180iterations finished qdiffx linear iterations at : 02:25:46 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 2.0939554E-03 5.2215576E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 02:25:47 12.623u 0.217s 0:13.27 96.6% 0+0k 0+0io 0pf+0w