Mon Oct 10 14:21:50 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 14:21:50 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 790 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6176159 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 0.6176159 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.014022 assigned positive charge : 425.9553 centred at (gu) : 90.53777 89.27522 90.23270 assigned negative charge : -417.9423 centred at (gu) : 90.55016 89.18487 90.17705 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7148 nv = 96 ne = 84 npr = 57959 no. pairs analyzed = 57959 no. exposed pairs = 3628 no. arc points = 25288 no. surface atoms = 1229 nbur = 1623 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3774 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.4100000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2496 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2022169E-09 1.0241025E-08 midg,1,midg; midg,igrid,midg -1.2175370E-10 1.0253316E-08 1,midg,midg; igrid,midg,midg 6.1202461E-09 5.8449672E-09 gauss-seidel spectral radius is 0.9864484 estimated iterations to convergence 70 setup time was (sec) 0.7000000 now iterating at: 14:21:51 rms-change max change #iterations 0.1320665 19.76020 at 10iterations 1.1894423E-02 1.553288 at 20iterations 1.1044793E-03 0.1884918 at 30iterations 1.0011240E-04 1.4052391E-02 at 40iterations 9.3773615E-06 1.3637543E-03 at 50iterations finished qdiffx linear iterations at : 14:21:54 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.3773615E-06 1.3637543E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:21:55 4.241u 0.192s 0:04.79 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 Mon Oct 10 2011 at 14:21:55 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 790 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.852848 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 1.852848 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.014022 assigned positive charge : 425.9553 centred at (gu) : 91.61230 87.82500 90.69682 assigned negative charge : -417.9423 centred at (gu) : 91.65047 87.55410 90.53094 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 78146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25288 grid for indexing accessible points = 1.400000 m= 25366 mr = 53376 m= 3386 mr = 17625 m= 158 mr = 1844 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.7300000 number of dielectric boundary points 34178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21249 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) : 0.6176159 object centre at (A) : 29.85250 27.48450 35.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5972064E-03 1.9755742E-02 midg,1,midg; midg,igrid,midg 7.0292768E-03 2.5035920E-02 1,midg,midg; igrid,midg,midg 1.3779131E-02 1.2656211E-02 gauss-seidel spectral radius is 0.9985876 estimated iterations to convergence 211 setup time was (sec) 1.110000 now iterating at: 14:21:56 rms-change max change #iterations 4.243104 192.3846 at 10iterations 1.960883 73.86916 at 20iterations 0.9044067 29.54551 at 30iterations 0.4176749 13.88167 at 40iterations 0.1931029 6.234516 at 50iterations 8.9028805E-02 2.747673 at 60iterations 4.1114405E-02 1.272116 at 70iterations 1.9059099E-02 0.6431236 at 80iterations 8.8026775E-03 0.2830086 at 90iterations 4.0769679E-03 0.1260691 at 100iterations 1.8926635E-03 6.0675621E-02 at 110iterations 8.7516138E-04 2.8097153E-02 at 120iterations finished qdiffx linear iterations at : 14:22:04 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 8.7516138E-04 2.8097153E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 14:22:05 9.561u 0.218s 0:10.21 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 Mon Oct 10 2011 at 14:22:05 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 790 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.779272 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 2.779272 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.014022 assigned positive charge : 425.9553 centred at (gu) : 92.41821 86.73729 91.04537 assigned negative charge : -417.9423 centred at (gu) : 92.47575 86.33108 90.79630 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 181127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25288 grid for indexing accessible points = 1.400000 m= 84845 mr = 130022 m= 27171 mr = 67611 m= 5752 mr = 20533 m= 696 mr = 4012 m= 34 mr = 350 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 1.810000 number of dielectric boundary points 77084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 21718 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) : 1.852848 object centre at (A) : 29.85250 27.48450 35.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2483583 0.1178743 midg,1,midg; midg,igrid,midg 8.5954592E-02 0.2951587 1,midg,midg; igrid,midg,midg 0.2153283 0.2556840 gauss-seidel spectral radius is 0.9992548 estimated iterations to convergence 289 setup time was (sec) 2.190000 now iterating at: 14:22:08 rms-change max change #iterations 10.16282 284.0529 at 10iterations 5.958268 124.3220 at 20iterations 3.460327 79.20833 at 30iterations 2.007667 56.18615 at 40iterations 1.159878 25.04876 at 50iterations 0.6678237 12.39358 at 60iterations 0.3851762 7.435350 at 70iterations 0.2216595 4.583732 at 80iterations 0.1273432 2.463728 at 90iterations 7.3072448E-02 1.271803 at 100iterations 4.1903563E-02 0.7590942 at 110iterations 2.4108224E-02 0.4635048 at 120iterations 1.3822818E-02 0.2423172 at 130iterations 7.9358481E-03 0.1442337 at 140iterations 4.5425054E-03 7.9744339E-02 at 150iterations 2.6063875E-03 4.5631409E-02 at 160iterations 1.4957888E-03 2.7450562E-02 at 170iterations 8.5845008E-04 1.5235901E-02 at 180iterations finished qdiffx linear iterations at : 14:22:21 total time elapsed so far: 15.19000 # loops : 180 mean,max change (kT/e) : 8.5845008E-04 1.5235901E-02 energy calculations done at 15.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 14:22:21 15.457u 0.239s 0:16.17 96.9% 0+0k 0+0io 0pf+0w