Tue Oct 11 06:24:19 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 Tue Oct 11 2011 at 06:24:19 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8068537 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 0.8068537 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 89.91359 90.45926 89.83025 assigned negative charge : -200.5323 centred at (gu) : 90.05145 90.49730 89.53651 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 24542 no. pairs analyzed = 24542 no. exposed pairs = 1679 no. arc points = 12129 no. surface atoms = 584 nbur = 735 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 570 mr = 3716 m= 8 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1300000 number of dielectric boundary points 3175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 851 ## 64 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 6041 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4947151E-07 7.5175956E-07 midg,1,midg; midg,igrid,midg 2.0555500E-07 5.6785829E-08 1,midg,midg; igrid,midg,midg 4.4754495E-07 -1.6969344E-07 gauss-seidel spectral radius is 0.9919090 estimated iterations to convergence 90 setup time was (sec) 0.3200000 now iterating at: 06:24:20 rms-change max change #iterations 0.2754730 41.33068 at 10iterations 4.2931184E-02 5.686307 at 20iterations 6.9516944E-03 1.007092 at 30iterations 1.2062840E-03 0.1814499 at 40iterations 2.7136330E-04 4.1002274E-02 at 50iterations finished qdiffx linear iterations at : 06:24:23 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.7136330E-04 4.1002274E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 06:24:23 3.284u 0.157s 0:03.75 91.4% 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 06:24:23 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.420561 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 2.420561 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 89.74123 91.37817 89.49108 assigned negative charge : -200.5323 centred at (gu) : 90.15444 91.49222 88.60973 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 29666 mr = 46784 m= 7756 mr = 23214 m= 947 mr = 5649 m= 47 mr = 503 m= 0 mr = 15 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10107 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) : 0.8068537 object centre at (A) : 5.493500 59.56500 17.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8653518E-02 7.5355299E-02 midg,1,midg; midg,igrid,midg 1.1856548E-02 2.4769914E-03 1,midg,midg; igrid,midg,midg 7.9201601E-02 1.3827289E-02 gauss-seidel spectral radius is 0.9990003 estimated iterations to convergence 250 setup time was (sec) 0.5700000 now iterating at: 06:24:24 rms-change max change #iterations 4.623019 211.0422 at 10iterations 2.422219 84.12201 at 20iterations 1.269065 42.79247 at 30iterations 0.6601436 22.30939 at 40iterations 0.3451954 10.75144 at 50iterations 0.1812038 6.131717 at 60iterations 9.4601281E-02 2.772579 at 70iterations 4.9515814E-02 1.519047 at 80iterations 2.5929365E-02 0.7983093 at 90iterations 1.3588619E-02 0.4279652 at 100iterations 7.2081988E-03 0.2246246 at 110iterations 3.8594136E-03 0.1120453 at 120iterations finished qdiffx linear iterations at : 06:24:31 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 3.8594136E-03 0.1120453 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 06:24:32 7.652u 0.185s 0:08.41 93.1% 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 Tue Oct 11 2011 at 06:24:32 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 !!! WARNING: SEP 97 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.630842 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 3.630842 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 89.61195 92.06735 89.23676 assigned negative charge : -200.5323 centred at (gu) : 90.23170 92.23837 87.91462 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 87810 mr = 112456 m= 42113 mr = 74037 m= 15340 mr = 35526 m= 3920 mr = 12586 m= 636 mr = 2933 m= 69 mr = 414 m= 0 mr = 36 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 65574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 10128 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) : 2.420561 object centre at (A) : 5.493500 59.56500 17.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7482570 0.4650756 midg,1,midg; midg,igrid,midg 4.6993457E-02 3.3374563E-02 1,midg,midg; igrid,midg,midg 0.5557963 4.7060262E-02 gauss-seidel spectral radius is 0.9993312 estimated iterations to convergence 305 setup time was (sec) 1.310000 now iterating at: 06:24:33 rms-change max change #iterations 9.777107 261.2840 at 10iterations 5.912376 133.6443 at 20iterations 3.554383 86.66216 at 30iterations 2.136737 45.65896 at 40iterations 1.273452 26.82006 at 50iterations 0.7611836 16.13366 at 60iterations 0.4530541 7.946165 at 70iterations 0.2700132 5.041893 at 80iterations 0.1608637 3.063787 at 90iterations 9.5371045E-02 1.676863 at 100iterations 5.6730833E-02 1.086243 at 110iterations 3.3656549E-02 0.6009121 at 120iterations 2.0005362E-02 0.3755980 at 130iterations 1.1890907E-02 0.2114239 at 140iterations 7.0995572E-03 0.1413078 at 150iterations 4.2887651E-03 8.8060379E-02 at 160iterations 2.6432464E-03 5.2429199E-02 at 170iterations 1.6864975E-03 3.3332825E-02 at 180iterations finished qdiffx linear iterations at : 06:24:44 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 1.6864975E-03 3.3332825E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 06:24:45 12.464u 0.198s 0:13.00 97.3% 0+0k 0+0io 0pf+0w