Sat Oct 15 12:18:35 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 15 2011 at 12:18:35 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2299 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6542915 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 0.6542915 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.51401 assigned positive charge : 335.4113 centred at (gu) : 89.73618 90.44715 91.55637 assigned negative charge : -323.8981 centred at (gu) : 89.81312 90.38757 91.57800 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6838 nv = 96 ne = 84 npr = 46307 no. pairs analyzed = 46307 no. exposed pairs = 2996 no. arc points = 21043 no. surface atoms = 999 nbur = 1300 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3684 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3000000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2033 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0487013E-08 2.9991323E-08 midg,1,midg; midg,igrid,midg 1.5070544E-08 3.6602003E-08 1,midg,midg; igrid,midg,midg 3.7816136E-08 1.3255256E-08 gauss-seidel spectral radius is 0.9878743 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 12:18:36 rms-change max change #iterations 0.1522957 23.30208 at 10iterations 1.5969800E-02 2.536372 at 20iterations 1.7758949E-03 0.2692423 at 30iterations 3.2408340E-04 5.3812027E-02 at 40iterations 1.0666339E-04 1.9041061E-02 at 50iterations finished qdiffx linear iterations at : 12:18:40 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 1.0666339E-04 1.9041061E-02 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.210000 DelPhi exited at 12:18:41 5.210u 0.434s 0:05.92 95.2% 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 15 2011 at 12:18:41 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2299 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.962875 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 1.962875 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.51401 assigned positive charge : 335.4113 centred at (gu) : 89.20795 91.34106 94.66869 assigned negative charge : -323.8981 centred at (gu) : 89.43948 91.16270 94.73403 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21043 grid for indexing accessible points = 1.400000 m= 26736 mr = 49426 m= 4715 mr = 19496 m= 333 mr = 2953 m= 5 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2156 time to turn everything in is 0.6000000 number of dielectric boundary points 32432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17093 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) : 0.6542915 object centre at (A) : 0.4010000 29.53950 14.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1806569E-02 2.5072232E-02 midg,1,midg; midg,igrid,midg 1.3370899E-03 3.1836204E-02 1,midg,midg; igrid,midg,midg 5.5058043E-02 3.5031062E-02 gauss-seidel spectral radius is 0.9986899 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 12:18:42 rms-change max change #iterations 4.079556 198.1656 at 10iterations 1.943426 71.81212 at 20iterations 0.9185975 29.76367 at 30iterations 0.4393404 15.50854 at 40iterations 0.2083629 6.826999 at 50iterations 9.8612741E-02 3.298006 at 60iterations 4.6959430E-02 1.484717 at 70iterations 2.2364797E-02 0.6916189 at 80iterations 1.0689789E-02 0.3248520 at 90iterations 5.1125246E-03 0.1562536 at 100iterations 2.4843155E-03 7.9551220E-02 at 110iterations 1.2314754E-03 4.0255189E-02 at 120iterations finished qdiffx linear iterations at : 12:18:54 total time elapsed so far: 12.70000 # loops : 120 mean,max change (kT/e) : 1.2314754E-03 4.0255189E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 12:18:55 12.886u 0.520s 0:13.93 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 15 2011 at 12:18:55 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2299 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.944312 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 2.944312 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.51401 assigned positive charge : 335.4113 centred at (gu) : 88.81197 92.01153 97.00285 assigned negative charge : -323.8981 centred at (gu) : 89.15919 91.74406 97.10113 start vw surface at 0.1100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 167848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21043 grid for indexing accessible points = 1.400000 m= 85144 mr = 119946 m= 32280 mr = 69089 m= 8551 mr = 25683 m= 1338 mr = 6455 m= 97 mr = 912 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 7051 time to turn everything in is 1.640000 number of dielectric boundary points 73151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 17319 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) : 1.962875 object centre at (A) : 0.4010000 29.53950 14.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6929129 0.3080540 midg,1,midg; midg,igrid,midg -1.2284579E-02 0.2860347 1,midg,midg; igrid,midg,midg 0.5935833 0.2976101 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 12:18:57 rms-change max change #iterations 9.612309 343.5283 at 10iterations 5.681917 141.3906 at 20iterations 3.335008 85.44521 at 30iterations 1.953132 50.09166 at 40iterations 1.142624 21.36150 at 50iterations 0.6661724 13.08522 at 60iterations 0.3889596 9.110378 at 70iterations 0.2260340 4.925200 at 80iterations 0.1314857 2.765323 at 90iterations 7.6403297E-02 1.420551 at 100iterations 4.4269234E-02 0.8398256 at 110iterations 2.5731264E-02 0.4507790 at 120iterations 1.4914668E-02 0.2856202 at 130iterations 8.6806687E-03 0.1838684 at 140iterations 5.0666109E-03 9.4841003E-02 at 150iterations 2.9688706E-03 6.5347672E-02 at 160iterations 1.7647938E-03 3.3638000E-02 at 170iterations 1.0719439E-03 2.2609711E-02 at 180iterations finished qdiffx linear iterations at : 12:19:17 total time elapsed so far: 21.41000 # loops : 180 mean,max change (kT/e) : 1.0719439E-03 2.2609711E-02 energy calculations done at 21.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.57000 DelPhi exited at 12:19:17 21.573u 0.576s 0:22.58 98.0% 0+0k 0+0io 0pf+0w