Mon Oct 10 14:02:48 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 14:02:48 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! 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: ZN7 701 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: 0.6217037 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 0.6217037 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 390.2131 centred at (gu) : 88.43314 89.36888 89.97878 assigned negative charge : -386.7136 centred at (gu) : 88.33939 89.41318 89.86500 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6614 nv = 96 ne = 84 npr = 52477 no. pairs analyzed = 52477 no. exposed pairs = 3051 no. arc points = 21630 no. surface atoms = 1027 nbur = 1532 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3668 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2000000 number of dielectric boundary points 3199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2192 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9552611E-09 1.0804943E-08 midg,1,midg; midg,igrid,midg 7.0282411E-09 -2.5830531E-12 1,midg,midg; igrid,midg,midg -5.0837539E-09 6.7484867E-09 gauss-seidel spectral radius is 0.9865959 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 14:02:49 rms-change max change #iterations 0.1280949 21.07185 at 10iterations 1.1961561E-02 1.700920 at 20iterations 1.1297609E-03 0.1621647 at 30iterations 1.1337054E-04 1.6542435E-02 at 40iterations 1.2888179E-05 2.2907257E-03 at 50iterations finished qdiffx linear iterations at : 14:02:52 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2888179E-05 2.2907257E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:02:52 3.409u 0.186s 0:04.03 88.8% 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 14:02:52 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! 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: ZN7 701 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: 1.865111 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 1.865111 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 390.2131 centred at (gu) : 85.29885 88.10635 89.93594 assigned negative charge : -386.7136 centred at (gu) : 85.01773 88.23927 89.59489 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 grid for indexing accessible points = 1.400000 m= 25386 mr = 49840 m= 3731 mr = 18897 m= 181 mr = 2332 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2744 time to turn everything in is 0.3500000 number of dielectric boundary points 29352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19160 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) : 0.6217037 object centre at (A) : -7.174000 -0.5499992 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0063549E-02 2.8708763E-02 midg,1,midg; midg,igrid,midg 1.3183765E-02 1.4763977E-03 1,midg,midg; igrid,midg,midg -4.6211779E-03 3.1729881E-02 gauss-seidel spectral radius is 0.9985728 estimated iterations to convergence 210 setup time was (sec) 0.5600000 now iterating at: 14:02:53 rms-change max change #iterations 4.028047 187.2480 at 10iterations 1.851026 65.12653 at 20iterations 0.8514977 29.91547 at 30iterations 0.3919196 13.06328 at 40iterations 0.1810067 5.766869 at 50iterations 8.3281383E-02 2.961094 at 60iterations 3.8420212E-02 1.297049 at 70iterations 1.7655944E-02 0.6204681 at 80iterations 8.1386520E-03 0.2631283 at 90iterations 3.7554610E-03 0.1213112 at 100iterations 1.7330660E-03 6.3884735E-02 at 110iterations 8.0263248E-04 2.9075146E-02 at 120iterations finished qdiffx linear iterations at : 14:03:00 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 8.0263248E-04 2.9075146E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 14:03:01 7.818u 0.206s 0:08.34 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 14:03:01 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! 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: ZN7 701 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: 2.797667 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 2.797667 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 390.2131 centred at (gu) : 82.94839 87.15952 89.90379 assigned negative charge : -386.7136 centred at (gu) : 82.52656 87.35889 89.39223 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 164592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 grid for indexing accessible points = 1.400000 m= 83363 mr = 120390 m= 29050 mr = 68802 m= 6631 mr = 23476 m= 802 mr = 4958 m= 25 mr = 517 m= 0 mr = 4 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 9548 time to turn everything in is 0.9100000 number of dielectric boundary points 66316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19534 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) : 1.865111 object centre at (A) : -7.174000 -0.5499992 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1543241 0.3937822 midg,1,midg; midg,igrid,midg 0.1734772 1.8528013E-02 1,midg,midg; igrid,midg,midg -2.5201289E-02 0.4007507 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 1.140000 now iterating at: 14:03:03 rms-change max change #iterations 9.511807 376.4766 at 10iterations 5.483059 118.9912 at 20iterations 3.137738 57.09378 at 30iterations 1.794424 34.26302 at 40iterations 1.023931 20.34042 at 50iterations 0.5856382 10.39668 at 60iterations 0.3343275 6.556754 at 70iterations 0.1903848 3.752247 at 80iterations 0.1082749 2.173766 at 90iterations 6.1791550E-02 1.185634 at 100iterations 3.5193332E-02 0.6625919 at 110iterations 2.0034188E-02 0.3479881 at 120iterations 1.1430214E-02 0.2132072 at 130iterations 6.5125357E-03 0.1267643 at 140iterations 3.7180013E-03 7.0437908E-02 at 150iterations 2.1206280E-03 4.1482925E-02 at 160iterations 1.2149619E-03 2.3336411E-02 at 170iterations 7.0125470E-04 1.3764381E-02 at 180iterations finished qdiffx linear iterations at : 14:03:14 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 7.0125470E-04 1.3764381E-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) 12.57000 DelPhi exited at 14:03:15 12.575u 0.226s 0:13.27 96.3% 0+0k 0+0io 0pf+0w