Wed Feb 15 08:56:45 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_thinner.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 Wed Feb 15 2012 at 08:56:45 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 = 2569 !!! WARNING: GLU 264 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6383704 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 0.6383704 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 91.45421 90.83675 89.23284 assigned negative charge : -376.4587 centred at (gu) : 91.40857 90.86954 89.42899 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6909 nv = 96 ne = 84 npr = 53147 no. pairs analyzed = 53147 no. exposed pairs = 3592 no. arc points = 24838 no. surface atoms = 1187 nbur = 1382 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 3487 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6710525E-08 -1.6695862E-08 midg,1,midg; midg,igrid,midg 4.5139772E-09 -2.0434863E-09 1,midg,midg; igrid,midg,midg -2.2195716E-09 9.2840713E-09 gauss-seidel spectral radius is 0.9872894 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:56:46 rms-change max change #iterations 0.1382823 22.95827 at 10iterations 1.3489128E-02 2.132315 at 20iterations 1.4300377E-03 0.1901159 at 30iterations 2.4028908E-04 3.4412384E-02 at 40iterations 7.2100054E-05 1.0055542E-02 at 50iterations finished qdiffx linear iterations at : 08:56:49 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 7.2100054E-05 1.0055542E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 08:56:49 3.794u 0.189s 0:04.35 91.2% 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 Wed Feb 15 2012 at 08:56:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 !!! WARNING: GLU 264 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.915111 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 1.915111 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 94.36208 92.50967 87.69772 assigned negative charge : -376.4587 centred at (gu) : 94.22541 92.60836 88.28683 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24838 grid for indexing accessible points = 1.400000 m= 26847 mr = 48757 m= 4661 mr = 18923 m= 263 mr = 2764 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 348 time to turn everything in is 0.6100000 number of dielectric boundary points 35296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19131 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) : 0.6383704 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4570365E-02 -5.9971060E-03 midg,1,midg; midg,igrid,midg 7.4198088E-03 1.6010249E-03 1,midg,midg; igrid,midg,midg -5.4885051E-03 3.0544444E-03 gauss-seidel spectral radius is 0.9986567 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 08:56:52 rms-change max change #iterations 4.250968 179.2022 at 10iterations 1.998953 62.67818 at 20iterations 0.9475518 41.81493 at 30iterations 0.4464044 15.65551 at 40iterations 0.2108662 6.604706 at 50iterations 9.9316105E-02 3.217727 at 60iterations 4.6998899E-02 1.495270 at 70iterations 2.2231279E-02 0.7163658 at 80iterations 1.0525740E-02 0.3258209 at 90iterations 5.0252876E-03 0.1691179 at 100iterations 2.4155539E-03 7.9547882E-02 at 110iterations 1.1855881E-03 3.8883209E-02 at 120iterations finished qdiffx linear iterations at : 08:56:59 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.1855881E-03 3.8883209E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 08:56:59 8.191u 0.258s 0:10.11 83.4% 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 Wed Feb 15 2012 at 08:56:59 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 = 2569 !!! WARNING: GLU 264 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.872667 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 2.872667 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 96.54282 93.76431 86.54641 assigned negative charge : -376.4587 centred at (gu) : 96.33823 93.91255 87.43018 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 171124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24838 grid for indexing accessible points = 1.400000 m= 84489 mr = 119280 m= 32363 mr = 66728 m= 8396 mr = 25217 m= 1133 mr = 6106 m= 62 mr = 680 m= 0 mr = 18 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1238 time to turn everything in is 1.440000 number of dielectric boundary points 79538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19438 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) : 1.915111 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.103632 2.6009990E-02 midg,1,midg; midg,igrid,midg 0.1410341 5.6998100E-02 1,midg,midg; igrid,midg,midg -0.1516814 4.3493815E-02 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 1.740000 now iterating at: 08:57:01 rms-change max change #iterations 10.00490 336.7230 at 10iterations 5.900755 143.9889 at 20iterations 3.462471 68.73377 at 30iterations 2.022361 41.68742 at 40iterations 1.181475 24.20064 at 50iterations 0.6882026 12.32462 at 60iterations 0.3998193 10.17708 at 70iterations 0.2317638 4.274056 at 80iterations 0.1344994 2.484045 at 90iterations 7.7873796E-02 1.430921 at 100iterations 4.5065973E-02 0.8290100 at 110iterations 2.6036158E-02 0.4756718 at 120iterations 1.5038969E-02 0.3015060 at 130iterations 8.7108184E-03 0.1615009 at 140iterations 5.0369441E-03 8.8585854E-02 at 150iterations 2.9123412E-03 5.7432175E-02 at 160iterations 1.6914003E-03 3.0714989E-02 at 170iterations 9.8205940E-04 1.7675400E-02 at 180iterations finished qdiffx linear iterations at : 08:57:12 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 9.8205940E-04 1.7675400E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 08:57:12 12.228u 0.181s 0:12.84 96.5% 0+0k 0+0io 0pf+0w