Sat Oct 8 19:45:44 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 Sat Oct 8 2011 at 19:45:44 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 = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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: 0.6200038 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 0.6200038 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 88.49857 89.17464 89.55157 assigned negative charge : -389.8296 centred at (gu) : 88.38858 89.22489 89.42604 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6447 nv = 96 ne = 84 npr = 54873 no. pairs analyzed = 54873 no. exposed pairs = 3014 no. arc points = 21684 no. surface atoms = 1011 nbur = 1595 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3563 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.2000000 number of dielectric boundary points 3161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2229 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3199307E-09 1.0796232E-08 midg,1,midg; midg,igrid,midg 8.3995966E-09 2.9426778E-10 1,midg,midg; igrid,midg,midg -5.3306048E-09 7.8574454E-09 gauss-seidel spectral radius is 0.9865230 estimated iterations to convergence 71 setup time was (sec) 0.4400000 now iterating at: 19:45:45 rms-change max change #iterations 0.1283832 17.75470 at 10iterations 1.1792405E-02 1.868442 at 20iterations 1.0947530E-03 0.1546364 at 30iterations 1.0334782E-04 1.5663147E-02 at 40iterations 1.0286797E-05 1.8272400E-03 at 50iterations finished qdiffx linear iterations at : 19:45:48 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 1.0286797E-05 1.8272400E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 19:45:49 3.995u 0.275s 0:04.53 94.0% 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 Sat Oct 8 2011 at 19:45:49 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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: 1.860012 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 1.860012 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 85.49516 87.52377 88.65446 assigned negative charge : -389.8296 centred at (gu) : 85.16547 87.67442 88.27792 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21684 grid for indexing accessible points = 1.400000 m= 23973 mr = 48950 m= 3292 mr = 17478 m= 167 mr = 1981 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4173 time to turn everything in is 0.3800000 number of dielectric boundary points 29105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19319 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) : 0.6200038 object centre at (A) : -6.810000 -0.2850008 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3815015E-02 2.9288135E-02 midg,1,midg; midg,igrid,midg 1.0580899E-02 7.6916238E-04 1,midg,midg; igrid,midg,midg -9.0874912E-04 3.9408263E-02 gauss-seidel spectral radius is 0.9985642 estimated iterations to convergence 209 setup time was (sec) 0.6500000 now iterating at: 19:45:50 rms-change max change #iterations 4.034513 168.8170 at 10iterations 1.860074 63.26952 at 20iterations 0.8502218 29.12795 at 30iterations 0.3910305 12.40043 at 40iterations 0.1797523 6.128051 at 50iterations 8.2420528E-02 2.917900 at 60iterations 3.7998907E-02 1.228111 at 70iterations 1.7439865E-02 0.6345549 at 80iterations 8.0162426E-03 0.2594757 at 90iterations 3.6767698E-03 0.1214170 at 100iterations 1.6942053E-03 5.6026459E-02 at 110iterations 7.8182458E-04 2.7761936E-02 at 120iterations finished qdiffx linear iterations at : 19:45:58 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 7.8182458E-04 2.7761936E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 19:45:59 9.299u 0.295s 0:09.85 97.2% 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 8 2011 at 19:45:59 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 = 2606 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 643 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: 2.790017 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): -31.24900 17.62900 ymin,ymax (A): -23.60700 23.03700 zmin,zma (A): -12.37000 45.04900 x,y,z range (A): 48.87800 46.64400 57.41900 scale (grids/A): 2.790017 object centre (A): -6.810000 -0.2850008 16.33950 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 394.2351 centred at (gu) : 83.24259 86.28542 87.98158 assigned negative charge : -389.8296 centred at (gu) : 82.74818 86.51163 87.41689 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 162442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21684 grid for indexing accessible points = 1.400000 m= 79446 mr = 118458 m= 26597 mr = 65175 m= 5711 mr = 21084 m= 697 mr = 4216 m= 41 mr = 450 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 14154 time to turn everything in is 0.9100000 number of dielectric boundary points 65533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19695 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) : 1.860012 object centre at (A) : -6.810000 -0.2850008 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1697995 0.3617726 midg,1,midg; midg,igrid,midg 0.1363052 -9.0155071E-03 1,midg,midg; igrid,midg,midg -2.4888813E-02 0.4959998 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 19:46:00 rms-change max change #iterations 9.517419 339.8865 at 10iterations 5.469053 129.0214 at 20iterations 3.125721 69.16565 at 30iterations 1.783528 41.23301 at 40iterations 1.016960 18.76769 at 50iterations 0.5788572 13.79920 at 60iterations 0.3298801 6.846388 at 70iterations 0.1873133 3.820862 at 80iterations 0.1066352 2.032368 at 90iterations 6.0757294E-02 1.291948 at 100iterations 3.4555964E-02 0.7304001 at 110iterations 1.9645657E-02 0.3574219 at 120iterations 1.1145036E-02 0.2324104 at 130iterations 6.3424231E-03 0.1155090 at 140iterations 3.6082650E-03 6.9845200E-02 at 150iterations 2.0500727E-03 3.8598061E-02 at 160iterations 1.1681177E-03 2.2998810E-02 at 170iterations 6.6671980E-04 1.3740540E-02 at 180iterations finished qdiffx linear iterations at : 19:46:12 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 6.6671980E-04 1.3740540E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 19:46:13 13.651u 0.248s 0:14.20 97.8% 0+0k 0+0io 0pf+0w