Sun Oct 9 08:15:17 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 Sun Oct 9 2011 at 08:15:17 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3715 !!! WARNING: NAP 1038 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4393163 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): -30.10900 23.41300 ymin,ymax (A): -21.87400 59.16100 zmin,zma (A): -17.49100 49.97900 x,y,z range (A): 53.52200 81.03500 67.47000 scale (grids/A): 0.4393163 object centre (A): -3.348001 18.64350 16.24400 number of atom coordinates read : 3715 total number of charged atoms : 3430 net assigned charge : 11.00003 assigned positive charge : 537.7085 centred at (gu) : 91.33399 83.32468 89.94901 assigned negative charge : -526.7098 centred at (gu) : 91.38704 83.40228 89.94109 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4406 nv = 96 ne = 84 npr = 73790 no. pairs analyzed = 73790 no. exposed pairs = 4889 no. arc points = 35776 no. surface atoms = 1622 nbur = 2093 mkacc time = 0.1600000 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= 125 mr = 1987 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 2543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2831 ## 573 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 5860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0140376E-12 3.7262667E-12 midg,1,midg; midg,igrid,midg 5.9320965E-11 -5.3131853E-14 1,midg,midg; igrid,midg,midg 4.0895213E-12 8.6570036E-13 gauss-seidel spectral radius is 0.9735153 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 08:15:18 rms-change max change #iterations 2.6697189E-02 6.387093 at 10iterations 1.1758297E-03 0.2344313 at 20iterations 1.7415623E-04 3.1514645E-02 at 30iterations 3.6795987E-05 6.8531036E-03 at 40iterations 7.9029605E-06 1.4801025E-03 at 50iterations finished qdiffx linear iterations at : 08:15:21 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 7.9029605E-06 1.4801025E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 08:15:21 3.592u 0.189s 0:04.33 87.0% 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 Sun Oct 9 2011 at 08:15:21 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3715 !!! WARNING: NAP 1038 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.317949 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): -30.10900 23.41300 ymin,ymax (A): -21.87400 59.16100 zmin,zma (A): -17.49100 49.97900 x,y,z range (A): 53.52200 81.03500 67.47000 scale (grids/A): 1.317949 object centre (A): -3.348001 18.64350 16.24400 number of atom coordinates read : 3715 total number of charged atoms : 3430 net assigned charge : 11.00003 assigned positive charge : 537.7085 centred at (gu) : 94.00097 69.97333 89.84627 assigned negative charge : -526.7098 centred at (gu) : 94.16083 70.20650 89.82276 start vw surface at 0.1600000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 50968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 11322 mr = 32098 m= 594 mr = 6587 m= 8 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 0.4100000 number of dielectric boundary points 24109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 588 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 24133 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) : 0.4393163 object centre at (A) : -3.348001 18.64350 16.24400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3087449E-03 9.2770281E-04 midg,1,midg; midg,igrid,midg 1.6473781E-02 -1.2664519E-04 1,midg,midg; igrid,midg,midg 1.0095700E-03 2.6668924E-05 gauss-seidel spectral radius is 0.9971867 estimated iterations to convergence 150 setup time was (sec) 0.7200000 now iterating at: 08:15:22 rms-change max change #iterations 2.182753 141.9883 at 10iterations 0.7410844 34.36711 at 20iterations 0.2483215 14.22165 at 30iterations 8.4537663E-02 5.259521 at 40iterations 2.8494515E-02 1.425495 at 50iterations 9.6871378E-03 0.4796772 at 60iterations 3.3199249E-03 0.1586685 at 70iterations 1.1750697E-03 5.5831909E-02 at 80iterations 4.4016173E-04 2.2178650E-02 at 90iterations 1.8772975E-04 8.5649490E-03 at 100iterations 9.2807801E-05 4.2085648E-03 at 110iterations 5.0525756E-05 1.9454956E-03 at 120iterations finished qdiffx linear iterations at : 08:15:29 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 5.0525756E-05 1.9454956E-03 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 08:15:30 7.547u 0.276s 0:08.12 96.1% 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 Sun Oct 9 2011 at 08:15:30 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3715 !!! WARNING: NAP 1038 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.976923 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): -30.10900 23.41300 ymin,ymax (A): -21.87400 59.16100 zmin,zma (A): -17.49100 49.97900 x,y,z range (A): 53.52200 81.03500 67.47000 scale (grids/A): 1.976923 object centre (A): -3.348001 18.64350 16.24400 number of atom coordinates read : 3715 total number of charged atoms : 3430 net assigned charge : 11.00003 assigned positive charge : 537.7085 centred at (gu) : 96.00110 59.95987 89.76925 assigned negative charge : -526.7098 centred at (gu) : 96.24113 60.30959 89.73408 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 119042 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 44180 mr = 80277 m= 7920 mr = 31937 m= 587 mr = 4855 m= 14 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3619 time to turn everything in is 0.9000000 number of dielectric boundary points 54456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 27059 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) : 1.317949 object centre at (A) : -3.348001 18.64350 16.24400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0358588E-02 1.3958770E-02 midg,1,midg; midg,igrid,midg 0.4958679 5.6307781E-03 1,midg,midg; igrid,midg,midg 1.9844804E-02 -8.6568296E-03 gauss-seidel spectral radius is 0.9987639 estimated iterations to convergence 225 setup time was (sec) 1.220000 now iterating at: 08:15:31 rms-change max change #iterations 6.582727 259.9189 at 10iterations 3.332036 113.4568 at 20iterations 1.670251 61.25275 at 30iterations 0.8306625 25.47678 at 40iterations 0.4121242 13.07488 at 50iterations 0.2035923 7.178764 at 60iterations 0.1005416 3.169207 at 70iterations 4.9387336E-02 1.461743 at 80iterations 2.4234144E-02 0.8164444 at 90iterations 1.1917919E-02 0.3711052 at 100iterations 5.8371038E-03 0.1777108 at 110iterations 2.8614148E-03 8.2911491E-02 at 120iterations 1.4043243E-03 4.0437698E-02 at 130iterations 6.9089211E-04 2.1432638E-02 at 140iterations 3.4056243E-04 9.8266602E-03 at 150iterations 1.6990304E-04 4.4145584E-03 at 160iterations 8.6005370E-05 2.3517609E-03 at 170iterations 4.5017852E-05 1.1882782E-03 at 180iterations finished qdiffx linear iterations at : 08:15:42 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 4.5017852E-05 1.1882782E-03 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 08:15:42 12.197u 0.295s 0:12.80 97.5% 0+0k 0+0io 0pf+0w