Sat Oct 8 18:34:01 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 18:34:01 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! 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 : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.40547 89.13123 90.06761 assigned negative charge : -387.4045 centred at (gu) : 88.29449 89.17599 89.95776 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 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 = 0.1100000 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 = 0.1200000 no. cavity mid-points inaccessible to solvent = 173 time to turn everything in is 0.2900000 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 0.4000000 number of grid points assigned charge 8334 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6435115E-09 1.8386981E-08 midg,1,midg; midg,igrid,midg 1.3096453E-08 6.6504208E-10 1,midg,midg; igrid,midg,midg -9.9375219E-09 1.2997988E-08 gauss-seidel spectral radius is 0.9873082 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 18:34:01 rms-change max change #iterations 0.1484327 20.89516 at 10iterations 1.4515814E-02 2.097433 at 20iterations 1.4261478E-03 0.2109470 at 30iterations 1.4193256E-04 2.2155762E-02 at 40iterations 1.3883375E-05 2.0117760E-03 at 50iterations finished qdiffx linear iterations at : 18:34:04 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.3883375E-05 2.0117760E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 18:34:04 3.147u 0.165s 0:03.58 92.1% 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 18:34:04 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 = 2592 !!! 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: 1.917277 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 : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.21610 87.39328 90.20238 assigned negative charge : -387.4045 centred at (gu) : 84.88338 87.52776 89.87283 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 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 0.5200000 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 0.6400000 number of grid points assigned charge 19298 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 -1.8387977E-02 3.2201923E-02 midg,1,midg; midg,igrid,midg 1.5485590E-02 1.5035690E-03 1,midg,midg; igrid,midg,midg -6.5048276E-03 3.5683542E-02 gauss-seidel spectral radius is 0.9986450 estimated iterations to convergence 215 setup time was (sec) 0.8000000 now iterating at: 18:34:05 rms-change max change #iterations 4.252598 162.0349 at 10iterations 2.001850 64.42405 at 20iterations 0.9429973 30.69360 at 30iterations 0.4431037 13.67327 at 40iterations 0.2075022 6.439174 at 50iterations 9.7921923E-02 2.831724 at 60iterations 4.5873441E-02 1.535346 at 70iterations 2.1559542E-02 0.6916199 at 80iterations 1.0138278E-02 0.3348274 at 90iterations 4.7466238E-03 0.1603203 at 100iterations 2.2375979E-03 7.3678970E-02 at 110iterations 1.0517506E-03 3.4379959E-02 at 120iterations finished qdiffx linear iterations at : 18:34:11 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 1.0517506E-03 3.4379959E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 18:34:12 7.192u 0.185s 0:07.71 95.5% 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 18:34:12 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 = 2592 !!! 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: 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 : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.82405 86.08988 90.30337 assigned negative charge : -387.4045 centred at (gu) : 82.32494 86.29159 89.80918 start vw surface at 0.1500000 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 = 0.7300000 no. cavity mid-points inaccessible to solvent = 18475 time to turn everything in is 1.320000 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 1.450000 number of grid points assigned charge 19626 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 -0.1366196 0.5093265 midg,1,midg; midg,igrid,midg 0.1707284 5.8732899E-03 1,midg,midg; igrid,midg,midg -2.7207403E-02 0.4329186 gauss-seidel spectral radius is 0.9992537 estimated iterations to convergence 289 setup time was (sec) 1.610000 now iterating at: 18:34:14 rms-change max change #iterations 9.845064 412.9280 at 10iterations 5.664894 117.2937 at 20iterations 3.246449 67.71564 at 30iterations 1.856719 35.20925 at 40iterations 1.062057 20.41576 at 50iterations 0.6077515 10.90036 at 60iterations 0.3482198 6.240019 at 70iterations 0.1988005 3.492895 at 80iterations 0.1140761 2.066687 at 90iterations 6.5249987E-02 1.169817 at 100iterations 3.7295111E-02 0.6648645 at 110iterations 2.1385042E-02 0.3977699 at 120iterations 1.2220265E-02 0.2206039 at 130iterations 7.0053292E-03 0.1214981 at 140iterations 3.9984128E-03 6.8893433E-02 at 150iterations 2.2868493E-03 3.9760590E-02 at 160iterations 1.3108435E-03 2.4673462E-02 at 170iterations 7.5144478E-04 1.3549805E-02 at 180iterations finished qdiffx linear iterations at : 18:34:24 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 7.5144478E-04 1.3549805E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 18:34:24 11.728u 0.199s 0:12.19 97.7% 0+0k 0+0io 0pf+0w