Mon Oct 10 19:38:36 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+sph2.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 = amb2.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 19:38:36 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 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: 0.6420546 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 0.6420546 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.457983 assigned positive charge : 294.6292 centred at (gu) : 89.55817 88.12054 87.71107 assigned negative charge : -300.0871 centred at (gu) : 89.43286 88.21423 87.97037 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5727 nv = 96 ne = 84 npr = 42030 no. pairs analyzed = 42030 no. exposed pairs = 2837 no. arc points = 20471 no. surface atoms = 952 nbur = 1095 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 2791 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1914 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6691 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4857570E-08 -2.1099439E-08 midg,1,midg; midg,igrid,midg -1.4892991E-10 -1.2138317E-08 1,midg,midg; igrid,midg,midg -2.3151108E-08 2.3552089E-09 gauss-seidel spectral radius is 0.9873931 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 19:38:37 rms-change max change #iterations 0.1361568 24.15735 at 10iterations 1.3371078E-02 1.988869 at 20iterations 1.3188858E-03 0.1937790 at 30iterations 1.2808005E-04 2.2304535E-02 at 40iterations 1.3025557E-05 1.8692017E-03 at 50iterations finished qdiffx linear iterations at : 19:38:40 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.3025557E-05 1.8692017E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 19:38:40 3.378u 0.162s 0:03.86 91.4% 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 Mon Oct 10 2011 at 19:38:40 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 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: 1.926164 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 1.926164 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.457983 assigned positive charge : 294.6292 centred at (gu) : 88.67467 84.36178 83.13338 assigned negative charge : -300.0871 centred at (gu) : 88.29866 84.64278 83.91117 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20471 grid for indexing accessible points = 1.400000 m= 19522 mr = 39219 m= 2658 mr = 13349 m= 122 mr = 1514 m= 0 mr = 50 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 973 time to turn everything in is 0.3100000 number of dielectric boundary points 29583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 15100 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) : 0.6420546 object centre at (A) : -7.5999260E-02 5.480499 5.671000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4715555E-02 -3.7544485E-02 midg,1,midg; midg,igrid,midg -5.9635630E-03 -1.1781493E-02 1,midg,midg; igrid,midg,midg -1.3626347E-02 -1.8914076E-03 gauss-seidel spectral radius is 0.9986189 estimated iterations to convergence 213 setup time was (sec) 0.5300000 now iterating at: 19:38:41 rms-change max change #iterations 3.795779 152.0083 at 10iterations 1.775541 68.61573 at 20iterations 0.8224792 30.69053 at 30iterations 0.3823996 13.47372 at 40iterations 0.1780636 6.095745 at 50iterations 8.2831152E-02 3.054474 at 60iterations 3.8488846E-02 1.374405 at 70iterations 1.7896514E-02 0.6631603 at 80iterations 8.3443895E-03 0.3219986 at 90iterations 3.8770069E-03 0.1441116 at 100iterations 1.8133504E-03 6.5157890E-02 at 110iterations 8.4224332E-04 3.0158997E-02 at 120iterations finished qdiffx linear iterations at : 19:38:48 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 8.4224332E-04 3.0158997E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 19:38:48 7.785u 0.178s 0:08.28 96.0% 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 Mon Oct 10 2011 at 19:38:49 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 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: 2.889246 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): -20.93500 20.78300 ymin,ymax (A): -22.24300 33.20400 zmin,zma (A): -21.35400 32.69600 x,y,z range (A): 41.71800 55.44700 54.05000 scale (grids/A): 2.889246 object centre (A): -7.5999260E-02 5.480499 5.671000 number of atom coordinates read : 2047 total number of charged atoms : 1917 net assigned charge : -5.457983 assigned positive charge : 294.6292 centred at (gu) : 88.01188 81.54272 79.69999 assigned negative charge : -300.0871 centred at (gu) : 87.44815 81.96414 80.86678 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 141792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20471 grid for indexing accessible points = 1.400000 m= 64548 mr = 96040 m= 21273 mr = 50224 m= 4445 mr = 16185 m= 556 mr = 3188 m= 22 mr = 392 m= 0 mr = 11 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3219 time to turn everything in is 0.7800000 number of dielectric boundary points 66596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 15331 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) : 1.926164 object centre at (A) : -7.5999260E-02 5.480499 5.671000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8699667 -0.3452680 midg,1,midg; midg,igrid,midg -0.5197521 -0.1658966 1,midg,midg; igrid,midg,midg -0.1157032 -4.8694089E-02 gauss-seidel spectral radius is 0.9992632 estimated iterations to convergence 291 setup time was (sec) 1.010000 now iterating at: 19:38:50 rms-change max change #iterations 8.993525 380.2782 at 10iterations 5.253331 142.6096 at 20iterations 3.053062 68.35929 at 30iterations 1.761105 36.69922 at 40iterations 1.018197 22.21182 at 50iterations 0.5880475 11.49672 at 60iterations 0.3381107 6.957552 at 70iterations 0.1954223 4.560722 at 80iterations 0.1120381 2.284777 at 90iterations 6.4473346E-02 1.239281 at 100iterations 3.7032496E-02 0.8968959 at 110iterations 2.1252349E-02 0.4370575 at 120iterations 1.2209776E-02 0.2977867 at 130iterations 7.0152399E-03 0.1447010 at 140iterations 4.0343958E-03 8.6269379E-02 at 150iterations 2.3164283E-03 4.7748566E-02 at 160iterations 1.3264944E-03 2.9561996E-02 at 170iterations 7.6166121E-04 1.5323639E-02 at 180iterations finished qdiffx linear iterations at : 19:39:01 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 7.6166121E-04 1.5323639E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 19:39:01 12.464u 0.198s 0:12.94 97.7% 0+0k 0+0io 0pf+0w