Sat Oct 8 15:58:22 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 Sat Oct 8 2011 at 15:58:22 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: GLM 711 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6474493 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 0.6474493 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2206 net assigned charge : 4.906005 assigned positive charge : 340.0262 centred at (gu) : 89.93336 88.62420 90.23071 assigned negative charge : -335.1209 centred at (gu) : 90.00265 88.75541 90.24921 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6460 nv = 96 ne = 84 npr = 47434 no. pairs analyzed = 47434 no. exposed pairs = 2884 no. arc points = 19932 no. surface atoms = 991 nbur = 1323 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3567 m= 0 mr = 50 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1983 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0340654E-08 6.5914159E-09 midg,1,midg; midg,igrid,midg 3.2840102E-08 -5.6917595E-09 1,midg,midg; igrid,midg,midg 1.7269812E-08 -2.2516483E-12 gauss-seidel spectral radius is 0.9876133 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 15:58:23 rms-change max change #iterations 0.1436347 23.77143 at 10iterations 1.4887593E-02 2.254742 at 20iterations 1.5384656E-03 0.2294350 at 30iterations 1.7497936E-04 2.5810242E-02 at 40iterations 2.5342204E-05 4.2076111E-03 at 50iterations finished qdiffx linear iterations at : 15:58:26 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.5342204E-05 4.2076111E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 15:58:27 4.037u 0.254s 0:04.56 93.8% 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 Sat Oct 8 2011 at 15:58:27 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: GLM 711 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.942348 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 1.942348 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2206 net assigned charge : 4.906005 assigned positive charge : 340.0262 centred at (gu) : 89.79918 85.87206 90.69169 assigned negative charge : -335.1209 centred at (gu) : 90.00783 86.26613 90.74738 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69723 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19932 grid for indexing accessible points = 1.400000 m= 25172 mr = 48401 m= 4533 mr = 18443 m= 341 mr = 3022 m= 9 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 29777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17415 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) : 0.6474493 object centre at (A) : 23.05950 7.003000 8.850499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9514965E-02 6.7164684E-03 midg,1,midg; midg,igrid,midg 2.6815273E-02 -3.4520288E-03 1,midg,midg; igrid,midg,midg 9.4805239E-03 -3.2002743E-02 gauss-seidel spectral radius is 0.9986571 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 15:58:28 rms-change max change #iterations 4.087021 169.9066 at 10iterations 1.914267 71.97539 at 20iterations 0.8993943 27.96477 at 30iterations 0.4249445 13.79741 at 40iterations 0.1999367 6.804457 at 50iterations 9.4261087E-02 3.208789 at 60iterations 4.4420391E-02 1.484060 at 70iterations 2.0926559E-02 0.7064896 at 80iterations 9.8708300E-03 0.3074622 at 90iterations 4.6764105E-03 0.1580521 at 100iterations 2.2054801E-03 7.5671673E-02 at 110iterations 1.0443386E-03 3.2859325E-02 at 120iterations finished qdiffx linear iterations at : 15:58:36 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.0443386E-03 3.2859325E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 15:58:37 9.423u 0.294s 0:10.02 96.9% 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 Sat Oct 8 2011 at 15:58:37 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: GLM 711 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.913522 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 2.913522 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2206 net assigned charge : 4.906005 assigned positive charge : 340.0262 centred at (gu) : 89.69864 83.80796 91.03746 assigned negative charge : -335.1209 centred at (gu) : 90.01183 84.39928 91.12100 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 161358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19932 grid for indexing accessible points = 1.400000 m= 80390 mr = 117254 m= 30383 mr = 65461 m= 8416 mr = 24539 m= 1407 mr = 6590 m= 129 mr = 973 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 67193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 17647 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) : 1.942348 object centre at (A) : 23.05950 7.003000 8.850499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1276367 -1.2374518E-02 midg,1,midg; midg,igrid,midg 0.2180735 -5.9594028E-02 1,midg,midg; igrid,midg,midg 7.0129633E-02 -0.4231100 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.980000 now iterating at: 15:58:39 rms-change max change #iterations 9.579491 433.4235 at 10iterations 5.641788 155.5905 at 20iterations 3.278384 83.43861 at 30iterations 1.915634 37.14433 at 40iterations 1.114418 21.40556 at 50iterations 0.6447099 12.93097 at 60iterations 0.3730352 7.660275 at 70iterations 0.2153644 4.201444 at 80iterations 0.1242457 2.575820 at 90iterations 7.1644120E-02 1.474892 at 100iterations 4.1188560E-02 0.7428074 at 110iterations 2.3825118E-02 0.4444084 at 120iterations 1.3670744E-02 0.2709064 at 130iterations 7.8734672E-03 0.1440959 at 140iterations 4.5392844E-03 7.7537537E-02 at 150iterations 2.6096131E-03 5.1665306E-02 at 160iterations 1.5047104E-03 2.7267933E-02 at 170iterations 8.7017595E-04 1.7110825E-02 at 180iterations finished qdiffx linear iterations at : 15:58:52 total time elapsed so far: 15.54000 # loops : 180 mean,max change (kT/e) : 8.7017595E-04 1.7110825E-02 energy calculations done at 15.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 15:58:53 15.717u 0.302s 0:16.28 98.3% 0+0k 0+0io 0pf+0w