Mon Oct 10 14:10:15 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 14:10:15 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 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: 0.7236214 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 0.7236214 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999991 assigned positive charge : 273.5583 centred at (gu) : 92.17879 89.07205 89.04053 assigned negative charge : -275.5582 centred at (gu) : 92.18983 89.22028 89.03423 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 39272 no. pairs analyzed = 39272 no. exposed pairs = 2301 no. arc points = 16580 no. surface atoms = 779 nbur = 1110 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3764 m= 1 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.2400000 number of dielectric boundary points 3321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1436 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7307 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4618861E-08 -1.7781263E-08 midg,1,midg; midg,igrid,midg 7.8568156E-08 -9.8657914E-08 1,midg,midg; igrid,midg,midg -1.2379208E-08 -4.8130143E-08 gauss-seidel spectral radius is 0.9900279 estimated iterations to convergence 81 setup time was (sec) 0.5500000 now iterating at: 14:10:16 rms-change max change #iterations 0.2065324 36.52930 at 10iterations 2.6776452E-02 3.730297 at 20iterations 3.4126956E-03 0.5329895 at 30iterations 4.3957398E-04 5.7674408E-02 at 40iterations 5.6668930E-05 8.8634491E-03 at 50iterations finished qdiffx linear iterations at : 14:10:20 total time elapsed so far: 4.840000 # loops : 50 mean,max change (kT/e) : 5.6668930E-05 8.8634491E-03 energy calculations done at 4.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 14:10:21 5.008u 0.460s 0:05.93 92.0% 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 14:10:21 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 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: 2.170864 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 2.170864 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999991 assigned positive charge : 273.5583 centred at (gu) : 96.53664 87.21632 87.12142 assigned negative charge : -275.5582 centred at (gu) : 96.56960 87.66077 87.10293 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16580 grid for indexing accessible points = 1.400000 m= 27633 mr = 50374 m= 5485 mr = 20642 m= 524 mr = 3702 m= 12 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1738 time to turn everything in is 0.6100000 number of dielectric boundary points 30608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 13991 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) : 0.7236214 object centre at (A) : -1.548501 3.258000 28.78600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6591540E-02 -2.1072915E-02 midg,1,midg; midg,igrid,midg 7.4520707E-03 -1.1148721E-02 1,midg,midg; igrid,midg,midg -6.5092123E-03 -1.1083828E-02 gauss-seidel spectral radius is 0.9988632 estimated iterations to convergence 235 setup time was (sec) 0.9100000 now iterating at: 14:10:22 rms-change max change #iterations 4.468723 196.1160 at 10iterations 2.233126 72.37263 at 20iterations 1.111657 34.23359 at 30iterations 0.5567840 18.60704 at 40iterations 0.2777230 9.237979 at 50iterations 0.1399138 4.385103 at 60iterations 6.9973513E-02 2.075148 at 70iterations 3.5036653E-02 1.139579 at 80iterations 1.7423926E-02 0.5303421 at 90iterations 8.7267542E-03 0.2919598 at 100iterations 4.3704039E-03 0.1217948 at 110iterations 2.1894386E-03 6.7060471E-02 at 120iterations finished qdiffx linear iterations at : 14:10:32 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 2.1894386E-03 6.7060471E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 14:10:33 11.141u 0.487s 0:12.12 95.8% 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 Mon Oct 10 2011 at 14:10:33 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 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: 3.256296 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 3.256296 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999991 assigned positive charge : 273.5583 centred at (gu) : 99.80509 85.82452 85.68217 assigned negative charge : -275.5582 centred at (gu) : 99.85452 86.49122 85.65437 start vw surface at 0.1000000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 165801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16580 grid for indexing accessible points = 1.400000 m= 86142 mr = 121148 m= 35061 mr = 71259 m= 10580 mr = 28603 m= 2204 mr = 8243 m= 222 mr = 1551 m= 10 mr = 106 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 5929 time to turn everything in is 1.890000 number of dielectric boundary points 69111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 14060 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) : 2.170864 object centre at (A) : -1.548501 3.258000 28.78600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1741347 1.5643965E-02 midg,1,midg; midg,igrid,midg 7.2880469E-02 -0.1151998 1,midg,midg; igrid,midg,midg -4.5328159E-02 -3.2538213E-02 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.280000 now iterating at: 14:10:36 rms-change max change #iterations 9.793703 393.0778 at 10iterations 5.740134 120.3075 at 20iterations 3.347174 64.47184 at 30iterations 1.959300 42.05906 at 40iterations 1.144359 20.25511 at 50iterations 0.6669081 11.94538 at 60iterations 0.3890938 6.845558 at 70iterations 0.2270182 3.856629 at 80iterations 0.1324507 2.373520 at 90iterations 7.7076428E-02 1.416283 at 100iterations 4.4993415E-02 0.7433916 at 110iterations 2.6233044E-02 0.4405572 at 120iterations 1.5292532E-02 0.2915535 at 130iterations 8.9016296E-03 0.1495590 at 140iterations 5.1905764E-03 8.5086823E-02 at 150iterations 3.0360506E-03 5.1692963E-02 at 160iterations 1.7657370E-03 3.0477524E-02 at 170iterations 1.0309672E-03 1.8230438E-02 at 180iterations finished qdiffx linear iterations at : 14:10:53 total time elapsed so far: 19.90000 # loops : 180 mean,max change (kT/e) : 1.0309672E-03 1.8230438E-02 energy calculations done at 19.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.08000 DelPhi exited at 14:10:54 20.085u 0.540s 0:20.96 98.3% 0+0k 0+0io 0pf+0w