Thu Jan 19 13:33:03 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:08 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6963 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4323379 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): -5.005000 77.33801 ymin,ymax (A): -0.8119999 75.09200 zmin,zma (A): 165.4100 235.2330 x,y,z range (A): 82.34300 75.90400 69.82300 scale (grids/A): 0.4323379 object centre (A): 36.16650 37.14000 200.3215 number of atom coordinates read : 6963 total number of charged atoms : 6792 net assigned charge : 3.200042 assigned positive charge : 1056.002 centred at (gu) : 89.10562 90.13977 89.58805 assigned negative charge : -1052.810 centred at (gu) : 89.08473 90.19832 89.55438 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 141516 no. pairs analyzed = 141516 no. exposed pairs = 9183 no. arc points = 61902 no. surface atoms = 3099 nbur = 3864 mkacc time = 0.2500000 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 = 1.932000 m= 189 mr = 3532 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5120 ## 1019 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9512749E-12 2.8564629E-12 midg,1,midg; midg,igrid,midg 4.8339579E-12 -3.7295592E-12 1,midg,midg; igrid,midg,midg -1.0209079E-12 1.7569118E-12 gauss-seidel spectral radius is 0.9728592 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 13:33:12 rms-change max change #iterations 3.2071419E-02 5.603821 at 10iterations 2.1114796E-03 0.3627319 at 20iterations 7.4655726E-04 0.1411934 at 30iterations 3.0853349E-04 5.7006836E-02 at 40iterations 1.2826774E-04 2.3115158E-02 at 50iterations finished qdiffx linear iterations at : 13:33:21 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 1.2826774E-04 2.3115158E-02 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 13:33:23 3.789u 0.204s 0:15.55 25.5% 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 Thu Jan 19 2012 at 13:33:27 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6963 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.297014 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): -5.005000 77.33801 ymin,ymax (A): -0.8119999 75.09200 zmin,zma (A): 165.4100 235.2330 x,y,z range (A): 82.34300 75.90400 69.82300 scale (grids/A): 1.297014 object centre (A): 36.16650 37.14000 200.3215 number of atom coordinates read : 6963 total number of charged atoms : 6792 net assigned charge : 3.200042 assigned positive charge : 1056.002 centred at (gu) : 87.31478 90.41808 88.76235 assigned negative charge : -1052.810 centred at (gu) : 87.25335 90.59481 88.66300 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61902 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 20937 mr = 57585 m= 1095 mr = 12316 m= 12 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.4800000 number of dielectric boundary points 40216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1201 ## 45 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 47288 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) : 0.4323379 object centre at (A) : 36.16650 37.14000 200.3215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4442586E-04 -4.0919193E-05 midg,1,midg; midg,igrid,midg 2.9924097E-03 -5.5064764E-03 1,midg,midg; igrid,midg,midg 2.9518206E-03 5.0203954E-03 gauss-seidel spectral radius is 0.9974522 estimated iterations to convergence 158 setup time was (sec) 0.7100000 now iterating at: 13:33:30 rms-change max change #iterations 3.129236 170.0836 at 10iterations 1.111014 42.83958 at 20iterations 0.3937908 13.53094 at 30iterations 0.1397594 5.205677 at 40iterations 4.9890220E-02 1.752510 at 50iterations 1.7921284E-02 0.6749687 at 60iterations 6.6158636E-03 0.2407684 at 70iterations 2.6563718E-03 0.1059189 at 80iterations 1.3057338E-03 5.7689667E-02 at 90iterations 8.0439833E-04 3.4227371E-02 at 100iterations 5.5820995E-04 2.0897865E-02 at 110iterations 4.0164529E-04 1.4638901E-02 at 120iterations finished qdiffx linear iterations at : 13:33:48 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 4.0164529E-04 1.4638901E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 13:33:49 8.204u 0.221s 0:22.08 38.1% 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 Thu Jan 19 2012 at 13:33:49 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6963 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.945521 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): -5.005000 77.33801 ymin,ymax (A): -0.8119999 75.09200 zmin,zma (A): 165.4100 235.2330 x,y,z range (A): 82.34300 75.90400 69.82300 scale (grids/A): 1.945521 object centre (A): 36.16650 37.14000 200.3215 number of atom coordinates read : 6963 total number of charged atoms : 6792 net assigned charge : 3.200042 assigned positive charge : 1056.002 centred at (gu) : 85.97175 90.62645 88.14326 assigned negative charge : -1052.810 centred at (gu) : 85.87990 90.89222 87.99446 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 207282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61902 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 80114 mr = 144070 m= 14811 mr = 58576 m= 1022 mr = 9256 m= 19 mr = 379 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 1.090000 number of dielectric boundary points 90967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 53629 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) : 1.297014 object centre at (A) : 36.16650 37.14000 200.3215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1466678E-02 -6.6662356E-03 midg,1,midg; midg,igrid,midg 5.7777897E-02 -0.1288850 1,midg,midg; igrid,midg,midg 0.2504545 0.1993069 gauss-seidel spectral radius is 0.9990022 estimated iterations to convergence 250 setup time was (sec) 1.340000 now iterating at: 13:33:56 rms-change max change #iterations 9.652049 326.9350 at 10iterations 5.291713 122.0655 at 20iterations 2.859833 73.19962 at 30iterations 1.540339 34.21279 at 40iterations 0.8219400 18.60446 at 50iterations 0.4391591 9.974010 at 60iterations 0.2333882 5.183887 at 70iterations 0.1237697 2.624435 at 80iterations 6.5532006E-02 1.435711 at 90iterations 3.4618758E-02 0.7479610 at 100iterations 1.8267326E-02 0.3960054 at 110iterations 9.6759899E-03 0.2044110 at 120iterations 5.1202383E-03 0.1091614 at 130iterations 2.7122712E-03 5.5697441E-02 at 140iterations 1.4494371E-03 2.9815674E-02 at 150iterations 7.9136668E-04 1.6001701E-02 at 160iterations 4.4470234E-04 9.7351074E-03 at 170iterations 2.6649595E-04 6.8264008E-03 at 180iterations finished qdiffx linear iterations at : 13:34:29 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 2.6649595E-04 6.8264008E-03 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 13:34:30 13.526u 0.268s 0:42.29 32.5% 0+0k 0+0io 0pf+0w