Sat Oct 15 11:27:23 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 Sat Oct 15 2011 at 11:27:23 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 = 3608 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: 0.5626502 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 0.5626502 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 88.89059 86.26514 91.02016 assigned negative charge : -544.9257 centred at (gu) : 88.94273 86.20561 90.96233 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 72055 no. pairs analyzed = 72055 no. exposed pairs = 4650 no. arc points = 32590 no. surface atoms = 1560 nbur = 2048 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 323 mr = 3907 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3363 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0124014E-09 5.1658833E-10 midg,1,midg; midg,igrid,midg -3.3088825E-09 1.6406437E-10 1,midg,midg; igrid,midg,midg 4.2116721E-10 -9.2697083E-10 gauss-seidel spectral radius is 0.9837558 estimated iterations to convergence 65 setup time was (sec) 0.4700000 now iterating at: 11:27:23 rms-change max change #iterations 9.3445994E-02 15.19905 at 10iterations 6.8312972E-03 1.251907 at 20iterations 5.8371812E-04 9.1663837E-02 at 30iterations 8.9117966E-05 1.8284559E-02 at 40iterations 2.2727671E-05 5.0044060E-03 at 50iterations finished qdiffx linear iterations at : 11:27:26 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.2727671E-05 5.0044060E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 11:27:27 3.472u 0.208s 0:03.99 91.9% 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 15 2011 at 11:27:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 1.687951 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 1.687951 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 86.67062 78.79427 93.05933 assigned negative charge : -544.9257 centred at (gu) : 86.82781 78.61627 92.88641 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32590 grid for indexing accessible points = 1.400000 m= 26769 mr = 56649 m= 3081 mr = 18358 m= 93 mr = 1540 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4100000 number of dielectric boundary points 36113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 26747 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) : 0.5626502 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3359755E-04 4.9932553E-03 midg,1,midg; midg,igrid,midg -3.6315005E-02 2.1021678E-03 1,midg,midg; igrid,midg,midg -1.2636362E-02 -3.4899771E-02 gauss-seidel spectral radius is 0.9983587 estimated iterations to convergence 196 setup time was (sec) 0.6400000 now iterating at: 11:27:28 rms-change max change #iterations 3.959668 184.2439 at 10iterations 1.715535 56.60633 at 20iterations 0.7517650 24.25996 at 30iterations 0.3261729 11.68315 at 40iterations 0.1423869 4.450478 at 50iterations 6.2011987E-02 2.306831 at 60iterations 2.7005801E-02 0.9193141 at 70iterations 1.1783097E-02 0.3666072 at 80iterations 5.1430673E-03 0.1715889 at 90iterations 2.2498302E-03 6.9459915E-02 at 100iterations 9.8570343E-04 3.3341885E-02 at 110iterations 4.3880526E-04 1.3801575E-02 at 120iterations finished qdiffx linear iterations at : 11:27:38 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 4.3880526E-04 1.3801575E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 11:27:39 7.994u 0.196s 0:11.75 69.6% 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 Sat Oct 15 2011 at 11:27:39 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 = 3608 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: 2.531926 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 2.531926 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 85.00583 73.19131 94.58884 assigned negative charge : -544.9257 centred at (gu) : 85.24160 72.92420 94.32955 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 191977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32590 grid for indexing accessible points = 1.400000 m= 91290 mr = 138232 m= 27180 mr = 72410 m= 4932 mr = 20353 m= 359 mr = 3157 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 1.000000 number of dielectric boundary points 81468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 27660 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) : 1.687951 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0846524E-02 0.2595514 midg,1,midg; midg,igrid,midg -0.5173843 1.7793935E-02 1,midg,midg; igrid,midg,midg -0.1841991 -0.6528724 gauss-seidel spectral radius is 0.9992056 estimated iterations to convergence 280 setup time was (sec) 1.230000 now iterating at: 11:27:41 rms-change max change #iterations 10.11584 329.7051 at 10iterations 5.823127 126.9958 at 20iterations 3.331063 84.35216 at 30iterations 1.899722 39.84050 at 40iterations 1.075551 22.06834 at 50iterations 0.6115027 11.86488 at 60iterations 0.3462172 6.716383 at 70iterations 0.1955545 3.672601 at 80iterations 0.1103077 2.085220 at 90iterations 6.2301051E-02 1.244200 at 100iterations 3.5139207E-02 0.6277962 at 110iterations 1.9825149E-02 0.3734798 at 120iterations 1.1178496E-02 0.2173600 at 130iterations 6.3138553E-03 0.1272058 at 140iterations 3.5555954E-03 6.4895630E-02 at 150iterations 2.0102821E-03 3.5940886E-02 at 160iterations 1.1377409E-03 2.0411491E-02 at 170iterations 6.4765470E-04 1.1280060E-02 at 180iterations finished qdiffx linear iterations at : 11:28:02 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 6.4765470E-04 1.1280060E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 11:28:03 13.469u 0.227s 0:24.14 56.6% 0+0k 0+0io 0pf+0w