Sat Oct 8 19:00:04 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 8 2011 at 19:00:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6187968 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 0.6187968 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 88.43208 89.20296 89.99667 assigned negative charge : -388.8705 centred at (gu) : 88.32387 89.23380 89.88845 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6683 nv = 96 ne = 84 npr = 53133 no. pairs analyzed = 53133 no. exposed pairs = 3043 no. arc points = 21877 no. surface atoms = 1034 nbur = 1568 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3731 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3400000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2179 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4294794E-09 1.0438297E-08 midg,1,midg; midg,igrid,midg 6.6226939E-09 1.3749478E-09 1,midg,midg; igrid,midg,midg -4.9876814E-09 7.4116473E-09 gauss-seidel spectral radius is 0.9864764 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 19:00:05 rms-change max change #iterations 0.1293697 18.50819 at 10iterations 1.1578036E-02 1.931370 at 20iterations 1.0874857E-03 0.1455078 at 30iterations 1.0169592E-04 1.4652252E-02 at 40iterations 9.4317174E-06 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 19:00:08 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.4317174E-06 1.6174316E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 19:00:09 4.178u 0.301s 0:04.77 93.7% 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 8 2011 at 19:00:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.856390 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 1.856390 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 85.29573 87.60845 89.98945 assigned negative charge : -388.8705 centred at (gu) : 84.97153 87.70090 89.66528 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 26314 mr = 50465 m= 4103 mr = 19771 m= 252 mr = 2652 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3751 time to turn everything in is 0.6600000 number of dielectric boundary points 29791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19290 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) : 0.6187968 object centre at (A) : -6.973000 -0.1444998 15.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8371921E-02 2.6481275E-02 midg,1,midg; midg,igrid,midg 1.3647040E-02 3.1731392E-03 1,midg,midg; igrid,midg,midg -3.9729802E-03 3.5267789E-02 gauss-seidel spectral radius is 0.9985664 estimated iterations to convergence 209 setup time was (sec) 0.9600000 now iterating at: 19:00:10 rms-change max change #iterations 4.034437 170.4290 at 10iterations 1.844173 70.57027 at 20iterations 0.8493443 31.04608 at 30iterations 0.3904594 13.15894 at 40iterations 0.1791980 6.294579 at 50iterations 8.2353480E-02 2.730366 at 60iterations 3.8015541E-02 1.230753 at 70iterations 1.7475715E-02 0.5435791 at 80iterations 8.0269631E-03 0.2666817 at 90iterations 3.6899114E-03 0.1142426 at 100iterations 1.6928384E-03 6.0684204E-02 at 110iterations 7.8183756E-04 2.4646759E-02 at 120iterations finished qdiffx linear iterations at : 19:00:19 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 7.8183756E-04 2.4646759E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 19:00:19 9.701u 0.335s 0:10.36 96.8% 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 Sat Oct 8 2011 at 19:00:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.784586 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 2.784586 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 82.94345 86.41248 89.98405 assigned negative charge : -388.8705 centred at (gu) : 82.45718 86.55125 89.49781 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 85479 mr = 121742 m= 30768 mr = 70850 m= 7415 mr = 24960 m= 1200 mr = 5734 m= 62 mr = 862 m= 0 mr = 23 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 12794 time to turn everything in is 1.650000 number of dielectric boundary points 67073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19694 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) : 1.856390 object centre at (A) : -6.973000 -0.1444998 15.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1507737 0.3926281 midg,1,midg; midg,igrid,midg 0.1637780 3.5302844E-02 1,midg,midg; igrid,midg,midg -1.2763881E-02 0.4387580 gauss-seidel spectral radius is 0.9992355 estimated iterations to convergence 285 setup time was (sec) 1.990000 now iterating at: 19:00:22 rms-change max change #iterations 9.505238 368.1274 at 10iterations 5.456160 115.8425 at 20iterations 3.125370 65.91681 at 30iterations 1.784429 33.18140 at 40iterations 1.017966 19.12046 at 50iterations 0.5798047 11.51346 at 60iterations 0.3306973 6.915387 at 70iterations 0.1881382 3.596616 at 80iterations 0.1071037 2.068718 at 90iterations 6.0960464E-02 1.263382 at 100iterations 3.4709625E-02 0.6395369 at 110iterations 1.9712346E-02 0.3543625 at 120iterations 1.1204909E-02 0.2010326 at 130iterations 6.3879993E-03 0.1279545 at 140iterations 3.6353136E-03 6.5078735E-02 at 150iterations 2.0645668E-03 3.9666176E-02 at 160iterations 1.1774629E-03 2.2491455E-02 at 170iterations 6.6995609E-04 1.2214661E-02 at 180iterations finished qdiffx linear iterations at : 19:00:36 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 6.6995609E-04 1.2214661E-02 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 19:00:36 16.332u 0.342s 0:16.98 98.1% 0+0k 0+0io 0pf+0w