Sat Oct 8 18:39:04 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 8 2011 at 18:39:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6141213 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 0.6141213 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.44000 89.23356 89.67353 assigned negative charge : -387.4045 centred at (gu) : 88.34052 89.26456 89.55720 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6327 nv = 96 ne = 84 npr = 54104 no. pairs analyzed = 54104 no. exposed pairs = 2930 no. arc points = 20840 no. surface atoms = 999 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3604 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.2800000 number of dielectric boundary points 3001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7833 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0707553E-09 8.5377154E-09 midg,1,midg; midg,igrid,midg 5.3406874E-09 9.1197183E-10 1,midg,midg; igrid,midg,midg -4.0852823E-09 5.8600440E-09 gauss-seidel spectral radius is 0.9862648 estimated iterations to convergence 70 setup time was (sec) 0.5000000 now iterating at: 18:39:04 rms-change max change #iterations 0.1233005 22.26009 at 10iterations 1.0868778E-02 1.767710 at 20iterations 9.7532297E-04 0.1397591 at 30iterations 8.7974622E-05 1.4364243E-02 at 40iterations 8.2277529E-06 1.1901855E-03 at 50iterations finished qdiffx linear iterations at : 18:39:07 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 8.2277529E-06 1.1901855E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 18:39:07 3.241u 0.207s 0:03.72 92.4% 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 8 2011 at 18:39:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.842364 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 1.842364 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.31949 87.70044 89.02045 assigned negative charge : -387.4045 centred at (gu) : 85.02151 87.79330 88.67148 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 24233 mr = 49132 m= 3338 mr = 18174 m= 175 mr = 2057 m= 0 mr = 79 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5917 time to turn everything in is 0.5000000 number of dielectric boundary points 27868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19211 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) : 0.6141213 object centre at (A) : -7.115000 -0.2915001 16.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6101794E-02 2.1513367E-02 midg,1,midg; midg,igrid,midg 1.1179214E-02 2.2673365E-03 1,midg,midg; igrid,midg,midg -5.7175378E-03 2.8376909E-02 gauss-seidel spectral radius is 0.9985366 estimated iterations to convergence 207 setup time was (sec) 0.7700000 now iterating at: 18:39:08 rms-change max change #iterations 3.959335 158.8568 at 10iterations 1.799824 64.02649 at 20iterations 0.8191164 28.10479 at 30iterations 0.3756046 12.54000 at 40iterations 0.1711731 6.034170 at 50iterations 7.8298680E-02 2.522243 at 60iterations 3.5651315E-02 1.379425 at 70iterations 1.6241396E-02 0.5327454 at 80iterations 7.4372739E-03 0.2353153 at 90iterations 3.3897632E-03 0.1080112 at 100iterations 1.5498552E-03 5.3092957E-02 at 110iterations 7.0817530E-04 2.2686958E-02 at 120iterations finished qdiffx linear iterations at : 18:39:15 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 7.0817530E-04 2.2686958E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 18:39:15 7.267u 0.239s 0:07.79 96.1% 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 8 2011 at 18:39:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: ZN5 556 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.763546 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 2.763546 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.97903 86.55046 88.53043 assigned negative charge : -387.4045 centred at (gu) : 82.53217 86.68991 88.00703 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 80708 mr = 118939 m= 27132 mr = 66987 m= 5871 mr = 21944 m= 781 mr = 4431 m= 46 mr = 541 m= 0 mr = 23 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 19679 time to turn everything in is 1.210000 number of dielectric boundary points 62856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 19627 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) : 1.842364 object centre at (A) : -7.115000 -0.2915001 16.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1202718 0.2672992 midg,1,midg; midg,igrid,midg 0.1532502 2.3149583E-02 1,midg,midg; igrid,midg,midg -5.8328707E-02 0.3756687 gauss-seidel spectral radius is 0.9992234 estimated iterations to convergence 283 setup time was (sec) 1.510000 now iterating at: 18:39:17 rms-change max change #iterations 9.309141 297.0197 at 10iterations 5.324955 113.9576 at 20iterations 3.027833 63.56439 at 30iterations 1.725121 35.24081 at 40iterations 0.9784011 19.07610 at 50iterations 0.5568588 10.36703 at 60iterations 0.3152294 6.034611 at 70iterations 0.1783347 3.642710 at 80iterations 0.1010780 1.962410 at 90iterations 5.7323650E-02 1.034910 at 100iterations 3.2446623E-02 0.5831971 at 110iterations 1.8399568E-02 0.3300591 at 120iterations 1.0410140E-02 0.2060413 at 130iterations 5.9030890E-03 0.1110535 at 140iterations 3.3449661E-03 6.3554764E-02 at 150iterations 1.8950378E-03 3.8055420E-02 at 160iterations 1.0722751E-03 2.0698547E-02 at 170iterations 6.0654763E-04 1.2060165E-02 at 180iterations finished qdiffx linear iterations at : 18:39:27 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 6.0654763E-04 1.2060165E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 18:39:28 11.820u 0.223s 0:12.31 97.8% 0+0k 0+0io 0pf+0w