Sun Oct 9 12:36:05 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+sph.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 = amb.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 12:36:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 0.6914232 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 0.6914232 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.05897 90.57100 90.40473 assigned negative charge : -356.4896 centred at (gu) : 89.06636 90.73250 90.45374 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7614 nv = 96 ne = 84 npr = 47629 no. pairs analyzed = 47629 no. exposed pairs = 2964 no. arc points = 20807 no. surface atoms = 985 nbur = 1381 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4222 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2000000 number of dielectric boundary points 3795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1914 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6600795E-08 1.2700795E-09 midg,1,midg; midg,igrid,midg 7.3815166E-08 -4.9309755E-08 1,midg,midg; igrid,midg,midg 2.8160478E-08 1.4773382E-08 gauss-seidel spectral radius is 0.9891313 estimated iterations to convergence 78 setup time was (sec) 0.4000000 now iterating at: 12:36:06 rms-change max change #iterations 0.1920706 26.01278 at 10iterations 2.3342529E-02 3.041067 at 20iterations 3.0126632E-03 0.4375687 at 30iterations 5.6489004E-04 8.4117889E-02 at 40iterations 1.5918196E-04 2.5604248E-02 at 50iterations finished qdiffx linear iterations at : 12:36:09 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.5918196E-04 2.5604248E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 12:36:09 3.525u 0.185s 0:03.96 93.4% 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 12:36:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 2.074270 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 2.074270 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 87.17641 91.71267 91.21363 assigned negative charge : -356.4896 centred at (gu) : 87.19891 92.19740 91.36097 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20807 grid for indexing accessible points = 1.400000 m= 30915 mr = 56176 m= 5323 mr = 22977 m= 454 mr = 3408 m= 3 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 0.4100000 number of dielectric boundary points 34911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17629 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) : 0.6914232 object centre at (A) : 19.50450 11.91400 23.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0977208E-02 1.2967821E-02 midg,1,midg; midg,igrid,midg 2.3061490E-02 -4.2608436E-02 1,midg,midg; igrid,midg,midg 3.5235927E-02 -6.4986506E-03 gauss-seidel spectral radius is 0.9988192 estimated iterations to convergence 230 setup time was (sec) 0.6200000 now iterating at: 12:36:10 rms-change max change #iterations 4.782382 199.7690 at 10iterations 2.345870 82.39674 at 20iterations 1.157873 37.61821 at 30iterations 0.5733913 18.72143 at 40iterations 0.2829921 9.303188 at 50iterations 0.1395075 4.185516 at 60iterations 6.8818443E-02 2.110792 at 70iterations 3.4217238E-02 1.061540 at 80iterations 1.6938739E-02 0.5383663 at 90iterations 8.5020550E-03 0.2384644 at 100iterations 4.2643417E-03 0.1235924 at 110iterations 2.1752059E-03 6.9587708E-02 at 120iterations finished qdiffx linear iterations at : 12:36:17 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.1752059E-03 6.9587708E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 12:36:18 8.096u 0.227s 0:08.59 96.7% 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 Sun Oct 9 2011 at 12:36:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 3.111405 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): -4.664000 43.67300 ymin,ymax (A): -13.83000 37.65800 zmin,zma (A): 2.163000 45.31700 x,y,z range (A): 48.33700 51.48800 43.15400 scale (grids/A): 3.111405 object centre (A): 19.50450 11.91400 23.74000 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 85.76462 92.56893 91.82043 assigned negative charge : -356.4896 centred at (gu) : 85.79829 93.29608 92.04139 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 186967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20807 grid for indexing accessible points = 1.400000 m= 98270 mr = 136022 m= 37554 mr = 80723 m= 9657 mr = 30331 m= 1811 mr = 7263 m= 171 mr = 1338 m= 0 mr = 98 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 5924 time to turn everything in is 1.240000 number of dielectric boundary points 78655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 17796 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) : 2.074270 object centre at (A) : 19.50450 11.91400 23.74000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4457607 3.0237356E-02 midg,1,midg; midg,igrid,midg 0.5231223 -0.4623732 1,midg,midg; igrid,midg,midg 0.3422474 -0.2902867 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 1.510000 now iterating at: 12:36:20 rms-change max change #iterations 10.78149 441.5984 at 10iterations 6.376025 127.1179 at 20iterations 3.764856 87.63035 at 30iterations 2.225557 42.52235 at 40iterations 1.309418 29.22533 at 50iterations 0.7692327 14.65027 at 60iterations 0.4514569 8.441869 at 70iterations 0.2647361 4.562568 at 80iterations 0.1552228 2.954796 at 90iterations 9.0800673E-02 1.634867 at 100iterations 5.3190622E-02 1.118668 at 110iterations 3.1204946E-02 0.5020938 at 120iterations 1.8434139E-02 0.3510456 at 130iterations 1.0947446E-02 0.1963517 at 140iterations 6.5984000E-03 0.1182785 at 150iterations 4.0779049E-03 8.2546234E-02 at 160iterations 2.6306831E-03 6.0295105E-02 at 170iterations 1.7895031E-03 3.8738251E-02 at 180iterations finished qdiffx linear iterations at : 12:36:32 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 1.7895031E-03 3.8738251E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 12:36:32 14.021u 0.270s 0:14.58 98.0% 0+0k 0+0io 0pf+0w