Sun Oct 9 07:50:13 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 Sun Oct 9 2011 at 07:50:13 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 0.6994381 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 0.6994381 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000020 assigned positive charge : 335.0884 centred at (gu) : 89.94743 90.67421 91.03764 assigned negative charge : -329.0889 centred at (gu) : 89.81929 90.75977 91.17587 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7403 nv = 96 ne = 84 npr = 45766 no. pairs analyzed = 45766 no. exposed pairs = 2717 no. arc points = 19460 no. surface atoms = 911 nbur = 1304 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4155 m= 6 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.2900000 number of dielectric boundary points 3659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1859 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3376094E-08 -2.2952840E-08 midg,1,midg; midg,igrid,midg 6.9935261E-08 5.7578040E-09 1,midg,midg; igrid,midg,midg -1.3725970E-08 9.6856937E-08 gauss-seidel spectral radius is 0.9893655 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 07:50:13 rms-change max change #iterations 0.2019466 28.42397 at 10iterations 2.4297128E-02 3.648506 at 20iterations 2.9302896E-03 0.4464369 at 30iterations 3.5182445E-04 4.3865204E-02 at 40iterations 4.2362684E-05 5.5866241E-03 at 50iterations finished qdiffx linear iterations at : 07:50:16 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.2362684E-05 5.5866241E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 07:50:17 3.474u 0.229s 0:03.99 92.4% 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 Sun Oct 9 2011 at 07:50:17 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.098314 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 2.098314 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000020 assigned positive charge : 335.0884 centred at (gu) : 89.84201 92.02250 93.11252 assigned negative charge : -329.0889 centred at (gu) : 89.45781 92.27927 93.52722 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 30865 mr = 53838 m= 6202 mr = 23592 m= 668 mr = 4207 m= 24 mr = 356 m= 0 mr = 6 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1798 time to turn everything in is 0.5800000 number of dielectric boundary points 33387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16499 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) : 0.6994381 object centre at (A) : 7.205501 5.157000 14.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1080914E-02 4.0406799E-03 midg,1,midg; midg,igrid,midg 2.8920714E-02 2.6602870E-02 1,midg,midg; igrid,midg,midg -1.4287362E-02 3.8939260E-02 gauss-seidel spectral radius is 0.9988267 estimated iterations to convergence 231 setup time was (sec) 0.8900000 now iterating at: 07:50:18 rms-change max change #iterations 4.744941 212.4027 at 10iterations 2.332197 82.25290 at 20iterations 1.155853 35.19796 at 30iterations 0.5738859 18.91727 at 40iterations 0.2836536 8.684148 at 50iterations 0.1405891 4.092457 at 60iterations 6.9458164E-02 2.271009 at 70iterations 3.4417100E-02 1.119229 at 80iterations 1.7043570E-02 0.5042229 at 90iterations 8.4806904E-03 0.2470545 at 100iterations 4.1837641E-03 0.1451344 at 110iterations 2.0664651E-03 6.3436508E-02 at 120iterations finished qdiffx linear iterations at : 07:50:25 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.0664651E-03 6.3436508E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 07:50:25 7.961u 0.244s 0:08.47 96.8% 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 Sun Oct 9 2011 at 07:50:25 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.147471 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): -16.35900 30.77000 ymin,ymax (A): -20.29200 30.60600 zmin,zma (A): -4.563000 34.36000 x,y,z range (A): 47.12900 50.89800 38.92300 scale (grids/A): 3.147471 object centre (A): 7.205501 5.157000 14.89850 number of atom coordinates read : 2215 total number of charged atoms : 2078 net assigned charge : 6.000020 assigned positive charge : 335.0884 centred at (gu) : 89.76312 93.03372 94.66869 assigned negative charge : -329.0889 centred at (gu) : 89.18671 93.41891 95.29083 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 178815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 95526 mr = 129693 m= 39851 mr = 79568 m= 11793 mr = 33102 m= 2565 mr = 9197 m= 347 mr = 1834 m= 25 mr = 251 m= 0 mr = 9 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 6098 time to turn everything in is 1.750000 number of dielectric boundary points 75268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 16624 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) : 2.098314 object centre at (A) : 7.205501 5.157000 14.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5987322 1.3453715E-02 midg,1,midg; midg,igrid,midg 0.1285601 0.3214738 1,midg,midg; igrid,midg,midg -6.8804443E-02 0.2699397 gauss-seidel spectral radius is 0.9992909 estimated iterations to convergence 296 setup time was (sec) 2.030000 now iterating at: 07:50:27 rms-change max change #iterations 10.43997 411.3750 at 10iterations 6.073194 131.6110 at 20iterations 3.534439 67.19963 at 30iterations 2.058987 37.33117 at 40iterations 1.194922 20.95222 at 50iterations 0.6955250 12.39150 at 60iterations 0.4039233 7.150665 at 70iterations 0.2345111 3.882275 at 80iterations 0.1360613 2.425833 at 90iterations 7.8945436E-02 1.396408 at 100iterations 4.5886472E-02 0.7727480 at 110iterations 2.6622072E-02 0.4526834 at 120iterations 1.5493903E-02 0.2650728 at 130iterations 8.9716502E-03 0.1499562 at 140iterations 5.2108113E-03 8.9199066E-02 at 150iterations 3.0319281E-03 5.0516129E-02 at 160iterations 1.7568582E-03 3.0431747E-02 at 170iterations 1.0226015E-03 1.7078400E-02 at 180iterations finished qdiffx linear iterations at : 07:50:37 total time elapsed so far: 11.47000 # loops : 180 mean,max change (kT/e) : 1.0226015E-03 1.7078400E-02 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 07:50:37 11.657u 0.152s 0:12.08 97.6% 0+0k 0+0io 0pf+0w