Mon Oct 10 14:37:16 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 Mon Oct 10 2011 at 14:37:16 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 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: 0.6471080 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): -2.343000 52.67100 ymin,ymax (A): 23.16200 71.58600 zmin,zma (A): -32.24400 18.65100 x,y,z range (A): 55.01400 48.42400 50.89500 scale (grids/A): 0.6471080 object centre (A): 25.16400 47.37400 -6.796500 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 361.2352 centred at (gu) : 88.96265 88.86848 90.19034 assigned negative charge : -363.7358 centred at (gu) : 89.14159 88.96944 90.08139 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6765 nv = 96 ne = 84 npr = 48870 no. pairs analyzed = 48870 no. exposed pairs = 3002 no. arc points = 20999 no. surface atoms = 1019 nbur = 1365 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3700 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2000 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8681964E-08 9.7579029E-09 midg,1,midg; midg,igrid,midg 1.0721251E-08 -1.4457618E-08 1,midg,midg; igrid,midg,midg 2.3026924E-08 -2.3248170E-08 gauss-seidel spectral radius is 0.9876105 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:37:16 rms-change max change #iterations 0.1519933 23.54522 at 10iterations 1.5943510E-02 2.227474 at 20iterations 1.8822938E-03 0.3425140 at 30iterations 4.0298101E-04 6.9856644E-02 at 40iterations 1.2910354E-04 2.3140907E-02 at 50iterations finished qdiffx linear iterations at : 14:37:19 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2910354E-04 2.3140907E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:37:20 3.414u 0.183s 0:04.02 89.3% 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 14:37:20 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 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: 1.941324 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): -2.343000 52.67100 ymin,ymax (A): 23.16200 71.58600 zmin,zma (A): -32.24400 18.65100 x,y,z range (A): 55.01400 48.42400 50.89500 scale (grids/A): 1.941324 object centre (A): 25.16400 47.37400 -6.796500 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 361.2352 centred at (gu) : 86.88766 86.60497 90.57074 assigned negative charge : -363.7358 centred at (gu) : 87.42468 86.90837 90.24406 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20999 grid for indexing accessible points = 1.400000 m= 26247 mr = 50587 m= 4201 mr = 19222 m= 296 mr = 2523 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 31238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17768 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) : 0.6471080 object centre at (A) : 25.16400 47.37400 -6.796500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1085251E-02 -6.6725621E-03 midg,1,midg; midg,igrid,midg 6.0433117E-03 -1.7255327E-02 1,midg,midg; igrid,midg,midg 4.0845569E-02 -9.8859007E-03 gauss-seidel spectral radius is 0.9986670 estimated iterations to convergence 217 setup time was (sec) 0.5900000 now iterating at: 14:37:21 rms-change max change #iterations 4.287497 164.2403 at 10iterations 2.026810 71.89954 at 20iterations 0.9569275 32.12300 at 30iterations 0.4507874 14.64617 at 40iterations 0.2140169 6.938265 at 50iterations 0.1008146 3.308020 at 60iterations 4.7709413E-02 1.471837 at 70iterations 2.2689082E-02 0.8032684 at 80iterations 1.0801685E-02 0.3310051 at 90iterations 5.1864008E-03 0.1778355 at 100iterations 2.5206627E-03 9.1142654E-02 at 110iterations 1.2630589E-03 4.4616699E-02 at 120iterations finished qdiffx linear iterations at : 14:37:28 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.2630589E-03 4.4616699E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 14:37:28 7.882u 0.199s 0:08.36 96.5% 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 14:37:28 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 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: 2.911986 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): -2.343000 52.67100 ymin,ymax (A): 23.16200 71.58600 zmin,zma (A): -32.24400 18.65100 x,y,z range (A): 55.01400 48.42400 50.89500 scale (grids/A): 2.911986 object centre (A): 25.16400 47.37400 -6.796500 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 361.2352 centred at (gu) : 85.33142 84.90742 90.85588 assigned negative charge : -363.7358 centred at (gu) : 86.13708 85.36240 90.36617 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 168701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20999 grid for indexing accessible points = 1.400000 m= 84771 mr = 122624 m= 30938 mr = 69174 m= 7558 mr = 24703 m= 1186 mr = 5451 m= 86 mr = 820 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 70436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18004 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) : 1.941324 object centre at (A) : 25.16400 47.37400 -6.796500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1328323 -0.2750739 midg,1,midg; midg,igrid,midg 0.1447924 -8.1444323E-02 1,midg,midg; igrid,midg,midg 0.5728891 3.8184162E-02 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 1.160000 now iterating at: 14:37:30 rms-change max change #iterations 9.972135 436.7583 at 10iterations 5.868108 140.9024 at 20iterations 3.422153 101.3707 at 30iterations 1.993797 38.63721 at 40iterations 1.158054 22.34933 at 50iterations 0.6700625 13.51302 at 60iterations 0.3886003 7.596576 at 70iterations 0.2246293 4.116884 at 80iterations 0.1296578 2.368097 at 90iterations 7.4846156E-02 1.496950 at 100iterations 4.3202259E-02 0.8340912 at 110iterations 2.4889439E-02 0.4496117 at 120iterations 1.4373221E-02 0.2738762 at 130iterations 8.3102630E-03 0.1457310 at 140iterations 4.8168506E-03 8.8363647E-02 at 150iterations 2.8195984E-03 5.5187225E-02 at 160iterations 1.6721985E-03 3.1199455E-02 at 170iterations 1.0209659E-03 2.0377159E-02 at 180iterations finished qdiffx linear iterations at : 14:37:41 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 1.0209659E-03 2.0377159E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 14:37:42 12.473u 0.201s 0:13.25 95.6% 0+0k 0+0io 0pf+0w