Tue Nov 22 14:10:02 PST 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 Tue Nov 22 2011 at 14:10:07 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6098605 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): -9.200000 49.17400 ymin,ymax (A): 8.813001 48.09300 zmin,zma (A): -3.664000 38.76800 x,y,z range (A): 58.37400 39.28000 42.43200 scale (grids/A): 0.6098605 object centre (A): 19.98700 28.45300 17.55200 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.16013 89.57368 90.52026 assigned negative charge : -283.6043 centred at (gu) : 90.13476 89.48781 90.62836 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4936 nv = 96 ne = 84 npr = 40324 no. pairs analyzed = 40324 no. exposed pairs = 2479 no. arc points = 17757 no. surface atoms = 839 nbur = 1129 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 208 mr = 2662 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1836 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0794303E-09 -1.1063649E-09 midg,1,midg; midg,igrid,midg -1.7665056E-10 5.4964078E-09 1,midg,midg; igrid,midg,midg 1.9933721E-09 4.0280592E-09 gauss-seidel spectral radius is 0.9860278 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 14:10:10 rms-change max change #iterations 9.9662282E-02 17.86078 at 10iterations 8.6974027E-03 1.493678 at 20iterations 7.7800045E-04 0.1313572 at 30iterations 6.7886314E-05 1.0909081E-02 at 40iterations 5.9833433E-06 9.4985962E-04 at 50iterations finished qdiffx linear iterations at : 14:10:22 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 5.9833433E-06 9.4985962E-04 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 14:10:23 4.357u 0.235s 0:17.33 26.4% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:10:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.829582 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): -9.200000 49.17400 ymin,ymax (A): 8.813001 48.09300 zmin,zma (A): -3.664000 38.76800 x,y,z range (A): 58.37400 39.28000 42.43200 scale (grids/A): 1.829582 object centre (A): 19.98700 28.45300 17.55200 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.48048 88.72105 91.56074 assigned negative charge : -283.6043 centred at (gu) : 90.40450 88.46353 91.88544 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 17809 mr = 36379 m= 2139 mr = 13147 m= 68 mr = 1190 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1589 time to turn everything in is 0.2800000 number of dielectric boundary points 22801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14335 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) : 0.6098605 object centre at (A) : 19.98700 28.45300 17.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4171593E-03 -1.7978337E-03 midg,1,midg; midg,igrid,midg 1.4247874E-03 6.9151740E-03 1,midg,midg; igrid,midg,midg 3.3015367E-02 3.8853124E-02 gauss-seidel spectral radius is 0.9984481 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 14:10:33 rms-change max change #iterations 3.278414 153.9760 at 10iterations 1.453450 58.26717 at 20iterations 0.6478516 26.02457 at 30iterations 0.2875621 12.47847 at 40iterations 0.1284624 4.561140 at 50iterations 5.7092104E-02 2.269455 at 60iterations 2.5395053E-02 1.013504 at 70iterations 1.1241280E-02 0.4486046 at 80iterations 5.0394395E-03 0.1954975 at 90iterations 2.2406690E-03 8.7821960E-02 at 100iterations 9.9759956E-04 4.0557861E-02 at 110iterations 4.4391348E-04 1.6576767E-02 at 120iterations finished qdiffx linear iterations at : 14:11:07 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 4.4391348E-04 1.6576767E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 14:11:08 9.710u 0.312s 0:41.10 24.3% 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 Tue Nov 22 2011 at 14:11:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.744372 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): -9.200000 49.17400 ymin,ymax (A): 8.813001 48.09300 zmin,zma (A): -3.664000 38.76800 x,y,z range (A): 58.37400 39.28000 42.43200 scale (grids/A): 2.744372 object centre (A): 19.98700 28.45300 17.55200 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.72079 88.08154 92.34124 assigned negative charge : -283.6043 centred at (gu) : 90.60690 87.69531 92.82819 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 123689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 59516 mr = 88256 m= 19089 mr = 48516 m= 3524 mr = 15260 m= 272 mr = 2515 m= 8 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 5331 time to turn everything in is 0.7300000 number of dielectric boundary points 51427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 14685 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) : 1.829582 object centre at (A) : 19.98700 28.45300 17.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9866775E-02 3.4841985E-04 midg,1,midg; midg,igrid,midg 4.1487627E-02 4.9659852E-02 1,midg,midg; igrid,midg,midg 0.3826689 0.3958821 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.060000 now iterating at: 14:11:19 rms-change max change #iterations 7.856729 330.9641 at 10iterations 4.444629 111.9122 at 20iterations 2.506833 58.83181 at 30iterations 1.402061 33.01215 at 40iterations 0.7859746 19.27158 at 50iterations 0.4400394 9.958520 at 60iterations 0.2457090 5.228348 at 70iterations 0.1369658 3.360916 at 80iterations 7.6702349E-02 1.700626 at 90iterations 4.2767469E-02 0.9494009 at 100iterations 2.3886532E-02 0.4835315 at 110iterations 1.3324376E-02 0.2883670 at 120iterations 7.4366638E-03 0.1659756 at 130iterations 4.1617407E-03 8.5731983E-02 at 140iterations 2.3258780E-03 5.0041199E-02 at 150iterations 1.2967674E-03 2.7540997E-02 at 160iterations 7.2397297E-04 1.5512943E-02 at 170iterations 4.0447642E-04 8.8357627E-03 at 180iterations finished qdiffx linear iterations at : 14:12:01 total time elapsed so far: 15.11000 # loops : 180 mean,max change (kT/e) : 4.0447642E-04 8.8357627E-03 energy calculations done at 15.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.24000 DelPhi exited at 14:12:04 15.245u 0.308s 0:51.39 30.2% 0+0k 0+0io 0pf+0w