Tue Oct 11 06:32:17 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 Tue Oct 11 2011 at 06:32:17 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7342931 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 0.7342931 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.0901 centred at (gu) : 89.99255 90.55256 88.96637 assigned negative charge : -298.1591 centred at (gu) : 89.80476 90.51118 88.89139 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7368 nv = 96 ne = 84 npr = 39716 no. pairs analyzed = 39716 no. exposed pairs = 2399 no. arc points = 16462 no. surface atoms = 813 nbur = 1181 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 572 mr = 4329 m= 7 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1545 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4587945E-08 1.2844474E-07 midg,1,midg; midg,igrid,midg 5.2692283E-08 1.4134760E-07 1,midg,midg; igrid,midg,midg -6.7959832E-08 2.4763986E-07 gauss-seidel spectral radius is 0.9903176 estimated iterations to convergence 83 setup time was (sec) 0.5200000 now iterating at: 06:32:18 rms-change max change #iterations 0.2273572 33.28031 at 10iterations 3.0903386E-02 4.011250 at 20iterations 4.2223777E-03 0.5018425 at 30iterations 6.2771764E-04 8.5023880E-02 at 40iterations 1.1769921E-04 1.3655663E-02 at 50iterations finished qdiffx linear iterations at : 06:32:22 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 1.1769921E-04 1.3655663E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 06:32:23 4.620u 0.398s 0:05.45 91.9% 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 Tue Oct 11 2011 at 06:32:23 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.202879 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 2.202879 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.0901 centred at (gu) : 89.97769 91.65776 86.89928 assigned negative charge : -298.1591 centred at (gu) : 89.41431 91.53371 86.67441 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 77814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16462 grid for indexing accessible points = 1.400000 m= 32127 mr = 55644 m= 6803 mr = 24658 m= 729 mr = 4632 m= 24 mr = 395 m= 0 mr = 7 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14979 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) : 0.7342931 object centre at (A) : 2.183001 -8.777000 12.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7587419E-02 4.4639427E-02 midg,1,midg; midg,igrid,midg 3.1470398E-03 4.1144304E-02 1,midg,midg; igrid,midg,midg 2.6365282E-02 5.5643830E-02 gauss-seidel spectral radius is 0.9988949 estimated iterations to convergence 238 setup time was (sec) 0.9700000 now iterating at: 06:32:24 rms-change max change #iterations 4.784945 206.5028 at 10iterations 2.417664 81.59558 at 20iterations 1.224807 36.40480 at 30iterations 0.6230366 18.82473 at 40iterations 0.3139542 8.991257 at 50iterations 0.1597238 4.405653 at 60iterations 8.0741234E-02 2.607004 at 70iterations 4.1045994E-02 1.187668 at 80iterations 2.0856546E-02 0.6429596 at 90iterations 1.0604517E-02 0.3343506 at 100iterations 5.4301815E-03 0.1600733 at 110iterations 2.7881246E-03 8.0934525E-02 at 120iterations finished qdiffx linear iterations at : 06:32:34 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 2.7881246E-03 8.0934525E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 06:32:35 11.523u 0.482s 0:12.55 95.6% 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 Tue Oct 11 2011 at 06:32:35 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.304319 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 3.304319 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.0901 centred at (gu) : 89.96650 92.48659 85.34888 assigned negative charge : -298.1591 centred at (gu) : 89.12150 92.30063 85.01172 start vw surface at 0.1000000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16462 grid for indexing accessible points = 1.400000 m= 99087 mr = 133745 m= 41842 mr = 82886 m= 12947 mr = 34788 m= 2744 mr = 10087 m= 388 mr = 2013 m= 23 mr = 271 m= 0 mr = 11 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 72709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15056 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) : 2.202879 object centre at (A) : 2.183001 -8.777000 12.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3074792 0.3384290 midg,1,midg; midg,igrid,midg 5.9136087E-03 0.3126329 1,midg,midg; igrid,midg,midg 0.3793771 0.4041825 gauss-seidel spectral radius is 0.9993079 estimated iterations to convergence 300 setup time was (sec) 2.370000 now iterating at: 06:32:38 rms-change max change #iterations 10.48698 299.3746 at 10iterations 6.232427 127.6392 at 20iterations 3.690516 76.23238 at 30iterations 2.190093 39.99849 at 40iterations 1.295693 23.03088 at 50iterations 0.7634883 12.95063 at 60iterations 0.4492293 8.370956 at 70iterations 0.2643292 4.787436 at 80iterations 0.1560719 2.614388 at 90iterations 9.1793954E-02 1.651834 at 100iterations 5.4154061E-02 0.8538246 at 110iterations 3.2072119E-02 0.5611725 at 120iterations 1.9138195E-02 0.3561478 at 130iterations 1.1531905E-02 0.2195473 at 140iterations 7.1373302E-03 0.1389790 at 150iterations 4.5750220E-03 8.5731506E-02 at 160iterations 3.0700318E-03 5.5747986E-02 at 170iterations 2.1899138E-03 4.0519714E-02 at 180iterations finished qdiffx linear iterations at : 06:32:54 total time elapsed so far: 18.76000 # loops : 180 mean,max change (kT/e) : 2.1899138E-03 4.0519714E-02 energy calculations done at 18.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.93000 DelPhi exited at 06:32:55 18.933u 0.466s 0:19.97 97.0% 0+0k 0+0io 0pf+0w