Sat Oct 8 15:02:36 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 15:02:36 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 !!! WARNING: GLM 475 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6216819 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 0.6216819 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3081 net assigned charge : 3.906006 assigned positive charge : 483.2438 centred at (gu) : 88.72324 88.60213 90.35995 assigned negative charge : -479.3391 centred at (gu) : 88.66238 88.59763 90.38422 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8181 nv = 96 ne = 84 npr = 67011 no. pairs analyzed = 67011 no. exposed pairs = 3644 no. arc points = 25509 no. surface atoms = 1238 nbur = 1992 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 4712 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2612 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0556586E-09 1.3926529E-09 midg,1,midg; midg,igrid,midg 4.0406469E-09 2.8061935E-09 1,midg,midg; igrid,midg,midg -2.5659894E-09 6.4950210E-09 gauss-seidel spectral radius is 0.9866496 estimated iterations to convergence 71 setup time was (sec) 0.6600000 now iterating at: 15:02:38 rms-change max change #iterations 0.1485978 18.06413 at 10iterations 1.4013260E-02 1.755974 at 20iterations 1.3809493E-03 0.1922264 at 30iterations 1.5227596E-04 1.8371582E-02 at 40iterations 2.2232900E-05 2.8533936E-03 at 50iterations finished qdiffx linear iterations at : 15:02:42 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 2.2232900E-05 2.8533936E-03 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 15:02:42 5.222u 0.478s 0:06.08 93.5% 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 Sat Oct 8 2011 at 15:02:43 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 !!! WARNING: GLM 475 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.865046 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 1.865046 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3081 net assigned charge : 3.906006 assigned positive charge : 483.2438 centred at (gu) : 86.16897 85.80566 91.07919 assigned negative charge : -479.3391 centred at (gu) : 85.98695 85.79240 91.15245 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 32405 mr = 65172 m= 4584 mr = 24144 m= 232 mr = 2778 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1237 time to turn everything in is 0.7200000 number of dielectric boundary points 35606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 24174 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) : 0.6216819 object centre at (A) : 75.17800 2.033501 27.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2913721E-02 -4.5889146E-03 midg,1,midg; midg,igrid,midg -2.8014211E-03 4.6388279E-03 1,midg,midg; igrid,midg,midg -2.0630841E-04 3.5566837E-02 gauss-seidel spectral radius is 0.9986326 estimated iterations to convergence 214 setup time was (sec) 1.130000 now iterating at: 15:02:44 rms-change max change #iterations 4.582151 164.6739 at 10iterations 2.139823 66.26550 at 20iterations 1.006100 31.01993 at 30iterations 0.4709751 14.34573 at 40iterations 0.2210274 6.545824 at 50iterations 0.1035167 2.969559 at 60iterations 4.8513349E-02 1.332230 at 70iterations 2.2816466E-02 0.6652088 at 80iterations 1.0693226E-02 0.2926521 at 90iterations 5.0221649E-03 0.1474838 at 100iterations 2.3506724E-03 6.5261841E-02 at 110iterations 1.1105713E-03 3.0071259E-02 at 120iterations finished qdiffx linear iterations at : 15:02:56 total time elapsed so far: 12.57000 # loops : 120 mean,max change (kT/e) : 1.1105713E-03 3.0071259E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 15:02:56 12.794u 0.540s 0:13.61 97.9% 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 15:02:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 !!! WARNING: GLM 475 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.797569 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 2.797569 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3081 net assigned charge : 3.906006 assigned positive charge : 483.2438 centred at (gu) : 84.25330 83.70832 91.61835 assigned negative charge : -479.3391 centred at (gu) : 83.98022 83.68858 91.72845 start vw surface at 0.1400000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 209978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 106990 mr = 157772 m= 36554 mr = 88611 m= 7941 mr = 29193 m= 946 mr = 5801 m= 41 mr = 576 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 3989 time to turn everything in is 2.000000 number of dielectric boundary points 80488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 24647 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) : 1.865046 object centre at (A) : 75.17800 2.033501 27.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2125775 -9.4979346E-02 midg,1,midg; midg,igrid,midg -0.2490801 2.5916813E-02 1,midg,midg; igrid,midg,midg 3.2024838E-02 0.3843798 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.390000 now iterating at: 15:02:59 rms-change max change #iterations 10.71186 357.0500 at 10iterations 6.231825 120.3863 at 20iterations 3.615251 70.73187 at 30iterations 2.088035 36.93130 at 40iterations 1.205047 22.62350 at 50iterations 0.6968168 11.55549 at 60iterations 0.4018128 7.199594 at 70iterations 0.2320099 3.574647 at 80iterations 0.1335175 2.102210 at 90iterations 7.6876432E-02 1.278499 at 100iterations 4.4319406E-02 0.7844353 at 110iterations 2.5554355E-02 0.4666795 at 120iterations 1.4753425E-02 0.2563591 at 130iterations 8.5095055E-03 0.1414642 at 140iterations 4.9332078E-03 8.2641602E-02 at 150iterations 2.8584541E-03 4.7462463E-02 at 160iterations 1.6694475E-03 2.9278755E-02 at 170iterations 9.8155544E-04 1.7091751E-02 at 180iterations finished qdiffx linear iterations at : 15:03:18 total time elapsed so far: 21.81000 # loops : 180 mean,max change (kT/e) : 9.8155544E-04 1.7091751E-02 energy calculations done at 21.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.99000 DelPhi exited at 15:03:19 21.990u 0.560s 0:22.81 98.8% 0+0k 0+0io 0pf+0w