Tue Oct 11 03:35:37 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 Tue Oct 11 2011 at 03:35:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6039733 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 0.6039733 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : 1.3798475E-05 assigned positive charge : 378.0669 centred at (gu) : 92.31932 89.78291 89.93087 assigned negative charge : -378.0674 centred at (gu) : 92.30543 90.05168 89.91180 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6212 nv = 96 ne = 84 npr = 48247 no. pairs analyzed = 48247 no. exposed pairs = 3478 no. arc points = 24943 no. surface atoms = 1155 nbur = 1343 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3057 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3000000 number of dielectric boundary points 3462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2415 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9990214E-10 7.2433010E-10 midg,1,midg; midg,igrid,midg 1.0915166E-08 -1.0554997E-08 1,midg,midg; igrid,midg,midg -3.4274755E-10 9.1020030E-10 gauss-seidel spectral radius is 0.9858133 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 03:35:37 rms-change max change #iterations 0.1073686 16.24181 at 10iterations 9.3047097E-03 1.407001 at 20iterations 7.9633819E-04 0.1199036 at 30iterations 7.0436981E-05 1.1497021E-02 at 40iterations 6.5820113E-06 9.2887878E-04 at 50iterations finished qdiffx linear iterations at : 03:35:40 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 6.5820113E-06 9.2887878E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:35:42 3.293u 0.179s 0:04.97 69.6% 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 Oct 11 2011 at 03:35:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 1.811920 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 1.811920 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : 1.3798475E-05 assigned positive charge : 378.0669 centred at (gu) : 96.95737 89.34811 89.79221 assigned negative charge : -378.0674 centred at (gu) : 96.91620 90.15464 89.73506 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24943 grid for indexing accessible points = 1.400000 m= 22152 mr = 43465 m= 3037 mr = 15111 m= 119 mr = 1659 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.5000000 number of dielectric boundary points 31904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18888 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) : 0.6039733 object centre at (A) : 36.94700 -1.479500 31.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0604983E-02 3.8612962E-03 midg,1,midg; midg,igrid,midg 3.7265193E-02 -4.8684217E-02 1,midg,midg; igrid,midg,midg 5.8546225E-03 2.4366377E-02 gauss-seidel spectral radius is 0.9985014 estimated iterations to convergence 205 setup time was (sec) 0.7900000 now iterating at: 03:35:43 rms-change max change #iterations 3.746114 176.6673 at 10iterations 1.686734 72.82474 at 20iterations 0.7607809 29.22284 at 30iterations 0.3432159 11.22954 at 40iterations 0.1542427 5.190048 at 50iterations 6.9538184E-02 2.345642 at 60iterations 3.1304341E-02 1.099255 at 70iterations 1.4118065E-02 0.4854584 at 80iterations 6.3863653E-03 0.2160034 at 90iterations 2.8782748E-03 0.1055145 at 100iterations 1.2995573E-03 4.5742989E-02 at 110iterations 5.8578188E-04 1.9130707E-02 at 120iterations finished qdiffx linear iterations at : 03:35:49 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 5.8578188E-04 1.9130707E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 03:35:50 7.439u 0.224s 0:08.24 92.8% 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 Tue Oct 11 2011 at 03:35:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.717880 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): 12.84500 61.04900 ymin,ymax (A): -30.95100 27.99200 zmin,zma (A): 3.101000 60.54500 x,y,z range (A): 48.20400 58.94300 57.44400 scale (grids/A): 2.717880 object centre (A): 36.94700 -1.479500 31.82300 number of atom coordinates read : 2498 total number of charged atoms : 2418 net assigned charge : 1.3798475E-05 assigned positive charge : 378.0669 centred at (gu) : 100.4359 89.02197 89.68829 assigned negative charge : -378.0674 centred at (gu) : 100.3742 90.23180 89.60259 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 154998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24943 grid for indexing accessible points = 1.400000 m= 71992 mr = 106528 m= 24627 mr = 56167 m= 5136 mr = 18746 m= 510 mr = 3470 m= 24 mr = 296 m= 0 mr = 6 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 1.200000 number of dielectric boundary points 72074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19341 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) : 1.811920 object centre at (A) : 36.94700 -1.479500 31.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3628793 0.5823538 midg,1,midg; midg,igrid,midg 0.5645042 -0.5415195 1,midg,midg; igrid,midg,midg 6.6653378E-02 0.2958355 gauss-seidel spectral radius is 0.9992322 estimated iterations to convergence 285 setup time was (sec) 1.510000 now iterating at: 03:35:52 rms-change max change #iterations 9.264639 265.4570 at 10iterations 5.404430 134.4174 at 20iterations 3.128422 75.37548 at 30iterations 1.808477 44.06338 at 40iterations 1.034975 23.86302 at 50iterations 0.5930281 13.24877 at 60iterations 0.3396277 8.151505 at 70iterations 0.1936157 4.125650 at 80iterations 0.1105347 2.294754 at 90iterations 6.2836893E-02 1.454273 at 100iterations 3.5754353E-02 0.7825428 at 110iterations 2.0357221E-02 0.4107509 at 120iterations 1.1581321E-02 0.2322731 at 130iterations 6.5783653E-03 0.1380882 at 140iterations 3.7373004E-03 7.6456070E-02 at 150iterations 2.1231843E-03 4.2320251E-02 at 160iterations 1.2064792E-03 2.3830414E-02 at 170iterations 6.8428076E-04 1.4026642E-02 at 180iterations finished qdiffx linear iterations at : 03:36:02 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 6.8428076E-04 1.4026642E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 03:36:03 12.226u 0.251s 0:13.01 95.8% 0+0k 0+0io 0pf+0w