Mon Oct 10 14:00:51 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 14:00:51 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! 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 702 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: 0.6193243 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 0.6193243 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 88.73644 89.36670 89.63257 assigned negative charge : -388.6046 centred at (gu) : 88.64393 89.41571 89.50443 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6341 nv = 96 ne = 84 npr = 54427 no. pairs analyzed = 54427 no. exposed pairs = 2988 no. arc points = 21422 no. surface atoms = 1005 nbur = 1573 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3487 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3500000 number of dielectric boundary points 3128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2176 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6761373E-09 1.0585520E-08 midg,1,midg; midg,igrid,midg 7.3896262E-09 6.0266403E-11 1,midg,midg; igrid,midg,midg -3.8361474E-09 6.9891724E-09 gauss-seidel spectral radius is 0.9864917 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 14:00:52 rms-change max change #iterations 0.1228904 20.88295 at 10iterations 1.1207364E-02 1.782955 at 20iterations 1.0221074E-03 0.1570787 at 30iterations 9.7051547E-05 1.3885498E-02 at 40iterations 8.8051320E-06 1.3313293E-03 at 50iterations finished qdiffx linear iterations at : 14:00:55 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 8.8051320E-06 1.3313293E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 14:00:56 4.098u 0.247s 0:04.75 91.1% 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 Mon Oct 10 2011 at 14:00:56 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! 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 702 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: 1.857973 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 1.857973 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 86.20878 88.09951 88.89708 assigned negative charge : -388.6046 centred at (gu) : 85.93143 88.24697 88.51310 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21422 grid for indexing accessible points = 1.400000 m= 23629 mr = 47963 m= 3500 mr = 17297 m= 185 mr = 2229 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3597 time to turn everything in is 0.6200000 number of dielectric boundary points 28800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19227 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) : 0.6193243 object centre at (A) : -7.363501 -0.5904999 16.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8148877E-02 2.9706607E-02 midg,1,midg; midg,igrid,midg 1.2689708E-02 1.0199137E-03 1,midg,midg; igrid,midg,midg -5.8199218E-03 3.4826327E-02 gauss-seidel spectral radius is 0.9985608 estimated iterations to convergence 209 setup time was (sec) 0.9200000 now iterating at: 14:00:57 rms-change max change #iterations 4.050795 199.8820 at 10iterations 1.855034 61.47627 at 20iterations 0.8494048 35.65382 at 30iterations 0.3905108 14.03361 at 40iterations 0.1796458 5.676521 at 50iterations 8.2488187E-02 2.973528 at 60iterations 3.7934277E-02 1.187309 at 70iterations 1.7401466E-02 0.6457825 at 80iterations 7.9464698E-03 0.2522526 at 90iterations 3.6618488E-03 0.1243591 at 100iterations 1.6778772E-03 5.5190563E-02 at 110iterations 7.7200512E-04 2.4471283E-02 at 120iterations finished qdiffx linear iterations at : 14:01:05 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 7.7200512E-04 2.4471283E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 14:01:06 9.357u 0.276s 0:10.15 94.7% 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 14:01:06 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! 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 702 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: 2.786959 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 2.786959 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 84.31297 87.14912 88.34554 assigned negative charge : -388.6046 centred at (gu) : 83.89719 87.37029 87.76958 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 160210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21422 grid for indexing accessible points = 1.400000 m= 78362 mr = 116613 m= 26498 mr = 64172 m= 6227 mr = 21225 m= 867 mr = 4695 m= 37 mr = 587 m= 0 mr = 15 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 12930 time to turn everything in is 1.540000 number of dielectric boundary points 64894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19630 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) : 1.857973 object centre at (A) : -7.363501 -0.5904999 16.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8808045E-02 0.4162921 midg,1,midg; midg,igrid,midg 0.1454238 -1.6221225E-02 1,midg,midg; igrid,midg,midg -5.3880539E-02 0.4532911 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.850000 now iterating at: 14:01:08 rms-change max change #iterations 9.477489 275.2401 at 10iterations 5.446449 112.2843 at 20iterations 3.111788 69.21642 at 30iterations 1.771975 41.59546 at 40iterations 1.007765 21.58554 at 50iterations 0.5741914 11.60351 at 60iterations 0.3258402 6.725531 at 70iterations 0.1851541 3.627625 at 80iterations 0.1051558 1.900719 at 90iterations 5.9901588E-02 1.111389 at 100iterations 3.3944447E-02 0.6638737 at 110iterations 1.9283477E-02 0.3720913 at 120iterations 1.0958322E-02 0.2067909 at 130iterations 6.2263710E-03 0.1234024 at 140iterations 3.5312292E-03 6.7623138E-02 at 150iterations 2.0080004E-03 3.9117336E-02 at 160iterations 1.1392517E-03 2.0475388E-02 at 170iterations 6.4735417E-04 1.2357712E-02 at 180iterations finished qdiffx linear iterations at : 14:01:22 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 6.4735417E-04 1.2357712E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 14:01:23 15.483u 0.319s 0:16.92 93.3% 0+0k 0+0io 0pf+0w