Mon Oct 10 14:01:04 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 14:01:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6746258 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): 22.97600 70.68000 ymin,ymax (A): -2.668000 50.10200 zmin,zma (A): -5.350000 37.06400 x,y,z range (A): 47.70400 52.77000 42.41400 scale (grids/A): 0.6746258 object centre (A): 46.82800 23.71700 15.85700 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 366.3661 centred at (gu) : 89.92966 89.49863 89.17056 assigned negative charge : -362.8665 centred at (gu) : 89.95790 89.33797 89.05268 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7228 nv = 96 ne = 84 npr = 47759 no. pairs analyzed = 47759 no. exposed pairs = 2959 no. arc points = 21008 no. surface atoms = 994 nbur = 1384 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3982 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2800000 number of dielectric boundary points 3620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1741458E-08 3.7784677E-08 midg,1,midg; midg,igrid,midg -3.3280578E-08 5.0377551E-08 1,midg,midg; igrid,midg,midg 2.1495950E-08 6.0553100E-09 gauss-seidel spectral radius is 0.9885874 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 14:01:05 rms-change max change #iterations 0.1768413 28.24383 at 10iterations 1.9514438E-02 2.546486 at 20iterations 2.2734194E-03 0.3079939 at 30iterations 3.0174127E-04 3.8791656E-02 at 40iterations 5.5879453E-05 8.1710815E-03 at 50iterations finished qdiffx linear iterations at : 14:01:07 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 5.5879453E-05 8.1710815E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 14:01:08 3.278u 0.189s 0:03.85 89.6% 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 14:01:08 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 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: 2.023877 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): 22.97600 70.68000 ymin,ymax (A): -2.668000 50.10200 zmin,zma (A): -5.350000 37.06400 x,y,z range (A): 47.70400 52.77000 42.41400 scale (grids/A): 2.023877 object centre (A): 46.82800 23.71700 15.85700 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 366.3661 centred at (gu) : 89.78844 88.49553 87.51131 assigned negative charge : -362.8665 centred at (gu) : 89.87352 88.01374 87.15788 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21008 grid for indexing accessible points = 1.400000 m= 28901 mr = 53724 m= 4727 mr = 21298 m= 348 mr = 2899 m= 3 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.5800000 number of dielectric boundary points 33367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17700 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) : 0.6746258 object centre at (A) : 46.82800 23.71700 15.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5071739E-03 4.9889423E-02 midg,1,midg; midg,igrid,midg -3.9750788E-02 2.1810681E-02 1,midg,midg; igrid,midg,midg 4.1017469E-02 -4.3732426E-03 gauss-seidel spectral radius is 0.9987659 estimated iterations to convergence 225 setup time was (sec) 0.8800000 now iterating at: 14:01:09 rms-change max change #iterations 4.625772 239.4902 at 10iterations 2.240322 75.75566 at 20iterations 1.090291 34.33486 at 30iterations 0.5288084 15.67945 at 40iterations 0.2573703 9.772609 at 50iterations 0.1251334 4.235733 at 60iterations 6.0774498E-02 1.987408 at 70iterations 2.9654082E-02 0.9505559 at 80iterations 1.4468206E-02 0.4699898 at 90iterations 7.0670638E-03 0.2132416 at 100iterations 3.4456553E-03 0.1135178 at 110iterations 1.6870425E-03 4.9975395E-02 at 120iterations finished qdiffx linear iterations at : 14:01:16 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.6870425E-03 4.9975395E-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) 7.870000 DelPhi exited at 14:01:17 7.872u 0.223s 0:08.95 90.3% 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 14:01:17 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.035816 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): 22.97600 70.68000 ymin,ymax (A): -2.668000 50.10200 zmin,zma (A): -5.350000 37.06400 x,y,z range (A): 47.70400 52.77000 42.41400 scale (grids/A): 3.035816 object centre (A): 46.82800 23.71700 15.85700 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 366.3661 centred at (gu) : 89.68265 87.74329 86.26693 assigned negative charge : -362.8665 centred at (gu) : 89.81023 87.02058 85.73682 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 178758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21008 grid for indexing accessible points = 1.400000 m= 92292 mr = 129878 m= 34361 mr = 75450 m= 8625 mr = 27667 m= 1484 mr = 6288 m= 145 mr = 1073 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 1.500000 number of dielectric boundary points 75230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 17888 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) : 2.023877 object centre at (A) : 46.82800 23.71700 15.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5197452E-02 0.4781628 midg,1,midg; midg,igrid,midg -0.3978228 0.4755837 1,midg,midg; igrid,midg,midg 0.5352300 -0.2219828 gauss-seidel spectral radius is 0.9992832 estimated iterations to convergence 295 setup time was (sec) 1.830000 now iterating at: 14:01:19 rms-change max change #iterations 10.55427 363.9455 at 10iterations 6.200786 121.2183 at 20iterations 3.640149 67.75220 at 30iterations 2.132715 42.18372 at 40iterations 1.247807 21.64957 at 50iterations 0.7284563 15.60149 at 60iterations 0.4248342 7.461342 at 70iterations 0.2473711 4.163786 at 80iterations 0.1438560 2.577026 at 90iterations 8.3671950E-02 1.470627 at 100iterations 4.8656944E-02 0.8792267 at 110iterations 2.8300757E-02 0.4887476 at 120iterations 1.6482262E-02 0.3115969 at 130iterations 9.5806159E-03 0.1699524 at 140iterations 5.6180716E-03 0.1015644 at 150iterations 3.3010414E-03 5.8283806E-02 at 160iterations 1.9558554E-03 3.5560608E-02 at 170iterations 1.1844421E-03 2.2186279E-02 at 180iterations finished qdiffx linear iterations at : 14:01:30 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.1844421E-03 2.2186279E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 14:01:31 12.850u 0.250s 0:13.98 93.7% 0+0k 0+0io 0pf+0w