Sat Oct 8 18:34:24 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 18:34:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! 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: 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6390923 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): -31.64300 17.38100 ymin,ymax (A): -23.44500 23.02100 zmin,zma (A): -12.13600 43.56800 x,y,z range (A): 49.02400 46.46600 55.70400 scale (grids/A): 0.6390923 object centre (A): -7.131000 -0.2119999 15.71600 number of atom coordinates read : 2592 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.41565 89.12646 90.07533 assigned negative charge : -387.9385 centred at (gu) : 88.30769 89.17101 89.96514 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6880 nv = 96 ne = 84 npr = 54808 no. pairs analyzed = 54808 no. exposed pairs = 2958 no. arc points = 20958 no. surface atoms = 999 nbur = 1593 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3908 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 173 time to turn everything in is 0.3000000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2018 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8323 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8262125E-09 1.8328707E-08 midg,1,midg; midg,igrid,midg 1.2919745E-08 5.6049188E-10 1,midg,midg; igrid,midg,midg -9.6380353E-09 1.2698274E-08 gauss-seidel spectral radius is 0.9873082 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 18:34:25 rms-change max change #iterations 0.1494541 21.30354 at 10iterations 1.4552421E-02 2.081814 at 20iterations 1.4310052E-03 0.2085133 at 30iterations 1.4277080E-04 2.2830009E-02 at 40iterations 1.3930830E-05 1.9941330E-03 at 50iterations finished qdiffx linear iterations at : 18:34:28 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.3930830E-05 1.9941330E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 18:34:28 3.214u 0.170s 0:03.67 92.0% 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 18:34:28 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! 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: 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.917277 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): -31.64300 17.38100 ymin,ymax (A): -23.44500 23.02100 zmin,zma (A): -12.13600 43.56800 x,y,z range (A): 49.02400 46.46600 55.70400 scale (grids/A): 1.917277 object centre (A): -7.131000 -0.2119999 15.71600 number of atom coordinates read : 2592 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.24664 87.37905 90.22554 assigned negative charge : -387.9385 centred at (gu) : 84.92300 87.51285 89.89501 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20958 grid for indexing accessible points = 1.400000 m= 26720 mr = 52796 m= 4008 mr = 20190 m= 266 mr = 2640 m= 6 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5281 time to turn everything in is 0.5500000 number of dielectric boundary points 30025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19267 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) : 0.6390923 object centre at (A) : -7.131000 -0.2119999 15.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8498128E-02 3.2318391E-02 midg,1,midg; midg,igrid,midg 1.5330573E-02 1.3831585E-03 1,midg,midg; igrid,midg,midg -6.4252149E-03 3.5015143E-02 gauss-seidel spectral radius is 0.9986450 estimated iterations to convergence 215 setup time was (sec) 0.8300000 now iterating at: 18:34:29 rms-change max change #iterations 4.265356 162.0349 at 10iterations 2.007930 64.42405 at 20iterations 0.9455621 30.00572 at 30iterations 0.4443890 13.75935 at 40iterations 0.2081509 6.584110 at 50iterations 9.8219581E-02 2.887036 at 60iterations 4.6004426E-02 1.526485 at 70iterations 2.1627199E-02 0.7063384 at 80iterations 1.0167328E-02 0.3382530 at 90iterations 4.7606360E-03 0.1603260 at 100iterations 2.2441540E-03 7.6501608E-02 at 110iterations 1.0552155E-03 3.4757614E-02 at 120iterations finished qdiffx linear iterations at : 18:34:36 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.0552155E-03 3.4757614E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 18:34:36 7.497u 0.199s 0:07.99 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 18:34:36 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! 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: 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: 2.875916 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): -31.64300 17.38100 ymin,ymax (A): -23.44500 23.02100 zmin,zma (A): -12.13600 43.56800 x,y,z range (A): 49.02400 46.46600 55.70400 scale (grids/A): 2.875916 object centre (A): -7.131000 -0.2119999 15.71600 number of atom coordinates read : 2592 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 82.86985 86.06854 90.33813 assigned negative charge : -387.9385 centred at (gu) : 82.38433 86.26923 89.84245 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 172687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20958 grid for indexing accessible points = 1.400000 m= 87396 mr = 127196 m= 31004 mr = 72865 m= 7206 mr = 25410 m= 1141 mr = 5598 m= 82 mr = 819 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 18475 time to turn everything in is 1.310000 number of dielectric boundary points 67578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 19594 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) : 1.917277 object centre at (A) : -7.131000 -0.2119999 15.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1375149 0.5112443 midg,1,midg; midg,igrid,midg 0.1694364 4.5571728E-03 1,midg,midg; igrid,midg,midg -2.6286667E-02 0.4254405 gauss-seidel spectral radius is 0.9992537 estimated iterations to convergence 289 setup time was (sec) 1.610000 now iterating at: 18:34:38 rms-change max change #iterations 9.875149 412.9280 at 10iterations 5.681422 117.2955 at 20iterations 3.256175 67.71763 at 30iterations 1.861922 35.13258 at 40iterations 1.065218 20.38262 at 50iterations 0.6094134 10.85459 at 60iterations 0.3491580 6.225645 at 70iterations 0.1993448 3.559690 at 80iterations 0.1143962 2.054898 at 90iterations 6.5420955E-02 1.169096 at 100iterations 3.7394162E-02 0.6695595 at 110iterations 2.1443691E-02 0.3960838 at 120iterations 1.2255222E-02 0.2240219 at 130iterations 7.0245243E-03 0.1227856 at 140iterations 4.0094927E-03 6.8180084E-02 at 150iterations 2.2933637E-03 4.0061951E-02 at 160iterations 1.3143937E-03 2.4112225E-02 at 170iterations 7.5342233E-04 1.3641357E-02 at 180iterations finished qdiffx linear iterations at : 18:34:49 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 7.5342233E-04 1.3641357E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 18:34:49 12.201u 0.217s 0:12.69 97.7% 0+0k 0+0io 0pf+0w