Mon Oct 10 09:44:59 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 09:44:59 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 = 2742 !!! WARNING: HIT 222 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: 0.5986614 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 0.5986614 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.014010 assigned positive charge : 401.1742 centred at (gu) : 88.84926 89.49360 89.61457 assigned negative charge : -399.1604 centred at (gu) : 88.98316 89.40525 89.55981 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 54200 no. pairs analyzed = 54200 no. exposed pairs = 4118 no. arc points = 29563 no. surface atoms = 1363 nbur = 1379 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 2965 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2818 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3024603E-09 2.5205140E-09 midg,1,midg; midg,igrid,midg -2.7225961E-09 3.5089884E-09 1,midg,midg; igrid,midg,midg 7.2258488E-09 -3.1335721E-09 gauss-seidel spectral radius is 0.9855879 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 09:45:00 rms-change max change #iterations 0.1107657 18.47743 at 10iterations 9.1038700E-03 1.380943 at 20iterations 7.5226079E-04 0.1183453 at 30iterations 6.6453096E-05 1.1010170E-02 at 40iterations 7.0243850E-06 1.0552406E-03 at 50iterations finished qdiffx linear iterations at : 09:45:03 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.0243850E-06 1.0552406E-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 09:45:03 3.416u 0.189s 0:03.92 91.5% 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 Mon Oct 10 2011 at 09:45:03 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 = 2742 !!! WARNING: HIT 222 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: 1.795984 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 1.795984 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.014010 assigned positive charge : 401.1742 centred at (gu) : 86.54748 88.48039 88.84340 assigned negative charge : -399.1604 centred at (gu) : 86.94916 88.21555 88.67899 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29563 grid for indexing accessible points = 1.400000 m= 23120 mr = 42926 m= 3430 mr = 14735 m= 164 mr = 1578 m= 4 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 37279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20234 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) : 0.5986614 object centre at (A) : 9.631499 -34.51400 22.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1225087E-03 -6.5661226E-03 midg,1,midg; midg,igrid,midg 2.1071700E-02 3.6738403E-02 1,midg,midg; igrid,midg,midg 2.2750260E-02 -7.7419272E-03 gauss-seidel spectral radius is 0.9985064 estimated iterations to convergence 205 setup time was (sec) 0.5700000 now iterating at: 09:45:04 rms-change max change #iterations 3.842297 169.3093 at 10iterations 1.727809 61.12383 at 20iterations 0.7815312 27.12961 at 30iterations 0.3527874 12.79858 at 40iterations 0.1593037 5.472674 at 50iterations 7.2253294E-02 2.686058 at 60iterations 3.2584850E-02 1.099072 at 70iterations 1.4725151E-02 0.5341339 at 80iterations 6.6822497E-03 0.2197280 at 90iterations 3.0022750E-03 0.1208229 at 100iterations 1.3577301E-03 4.7667503E-02 at 110iterations 6.1290473E-04 2.1377563E-02 at 120iterations finished qdiffx linear iterations at : 09:45:11 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 6.1290473E-04 2.1377563E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 09:45:12 7.838u 0.200s 0:08.38 95.8% 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 09:45:12 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIT 222 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: 2.693976 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 2.693976 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.014010 assigned positive charge : 401.1742 centred at (gu) : 84.82128 87.72065 88.26485 assigned negative charge : -399.1604 centred at (gu) : 85.42371 87.32323 88.01833 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29563 grid for indexing accessible points = 1.400000 m= 74337 mr = 105916 m= 25741 mr = 55317 m= 5538 mr = 18518 m= 579 mr = 3260 m= 33 mr = 250 m= 0 mr = 7 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 84230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 20730 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) : 1.795984 object centre at (A) : 9.631499 -34.51400 22.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6640260E-02 -6.7755915E-02 midg,1,midg; midg,igrid,midg 0.4564922 0.5425944 1,midg,midg; igrid,midg,midg 0.2701799 -5.4680999E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.130000 now iterating at: 09:45:13 rms-change max change #iterations 9.629092 272.1221 at 10iterations 5.716291 150.0401 at 20iterations 3.364372 95.39499 at 30iterations 1.961860 48.65111 at 40iterations 1.140899 26.32150 at 50iterations 0.6601152 16.13797 at 60iterations 0.3819668 9.101383 at 70iterations 0.2203243 4.826686 at 80iterations 0.1269398 2.777199 at 90iterations 7.3351033E-02 1.581805 at 100iterations 4.1993875E-02 0.9034309 at 110iterations 2.4143774E-02 0.6410577 at 120iterations 1.3863567E-02 0.3129916 at 130iterations 7.9389699E-03 0.1743279 at 140iterations 4.5585721E-03 9.8937988E-02 at 150iterations 2.6133291E-03 5.2499294E-02 at 160iterations 1.4993538E-03 2.9270172E-02 at 170iterations 8.5904927E-04 1.7930984E-02 at 180iterations finished qdiffx linear iterations at : 09:45:24 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 8.5904927E-04 1.7930984E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 09:45:25 12.746u 0.224s 0:13.26 97.7% 0+0k 0+0io 0pf+0w