Tue Oct 11 03:16:03 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 03:16:03 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 = 3199 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: 0.5346550 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 0.5346550 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 91.51295 92.92052 88.93777 assigned negative charge : -484.4519 centred at (gu) : 91.50127 92.95265 88.98200 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5711 nv = 96 ne = 84 npr = 66459 no. pairs analyzed = 66459 no. exposed pairs = 3978 no. arc points = 27194 no. surface atoms = 1346 nbur = 1853 mkacc time = 0.1100000 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 = 1.596000 m= 222 mr = 2990 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2757 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4406332E-11 -3.3635644E-10 midg,1,midg; midg,igrid,midg -4.4211725E-11 -8.0098073E-10 1,midg,midg; igrid,midg,midg -1.9782138E-10 -2.5786637E-10 gauss-seidel spectral radius is 0.9819825 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 03:16:04 rms-change max change #iterations 7.0166096E-02 10.62441 at 10iterations 4.4548139E-03 0.8253555 at 20iterations 3.8509787E-04 6.8749160E-02 at 30iterations 7.1449271E-05 1.7374039E-02 at 40iterations 1.9223589E-05 4.7564358E-03 at 50iterations finished qdiffx linear iterations at : 03:16:07 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.9223589E-05 4.7564358E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 03:16:07 3.501u 0.166s 0:03.97 92.1% 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 03:16:07 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 = 3199 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: 1.603965 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 1.603965 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 94.53821 98.76052 86.81232 assigned negative charge : -484.4519 centred at (gu) : 94.50363 98.85794 86.94576 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 63462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18984 mr = 42884 m= 1872 mr = 13116 m= 43 mr = 835 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.3300000 number of dielectric boundary points 27527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 349 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 23310 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) : 0.5346550 object centre at (A) : 26.53500 69.20149 85.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6371110E-03 -6.4084930E-03 midg,1,midg; midg,igrid,midg 2.2740852E-02 -1.4719864E-02 1,midg,midg; igrid,midg,midg -3.6379804E-03 5.5304565E-03 gauss-seidel spectral radius is 0.9981210 estimated iterations to convergence 183 setup time was (sec) 0.5500000 now iterating at: 03:16:08 rms-change max change #iterations 3.307973 152.3938 at 10iterations 1.357007 57.25603 at 20iterations 0.5558965 20.99480 at 30iterations 0.2285122 8.680562 at 40iterations 9.3861386E-02 3.725725 at 50iterations 3.8618259E-02 1.457701 at 60iterations 1.5893737E-02 0.6111609 at 70iterations 6.5333322E-03 0.2526379 at 80iterations 2.7200661E-03 9.8186493E-02 at 90iterations 1.1340554E-03 3.9052248E-02 at 100iterations 4.8731625E-04 1.8693328E-02 at 110iterations 2.1681392E-04 9.7502470E-03 at 120iterations finished qdiffx linear iterations at : 03:16:15 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.1681392E-04 9.7502470E-03 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 03:16:16 7.729u 0.196s 0:08.43 93.8% 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 03:16:16 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 = 3199 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: 2.405947 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 2.405947 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 96.80712 103.1408 85.21825 assigned negative charge : -484.4519 centred at (gu) : 96.75526 103.2868 85.41846 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 147683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66481 mr = 105425 m= 18405 mr = 52413 m= 2764 mr = 13676 m= 176 mr = 1679 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.7800000 number of dielectric boundary points 62250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 24435 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) : 1.603965 object centre at (A) : 26.53500 69.20149 85.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2157430E-02 -9.0235956E-02 midg,1,midg; midg,igrid,midg 0.4154413 -0.3820277 1,midg,midg; igrid,midg,midg -5.7328544E-03 0.1801020 gauss-seidel spectral radius is 0.9991171 estimated iterations to convergence 266 setup time was (sec) 1.010000 now iterating at: 03:16:17 rms-change max change #iterations 8.690816 340.6841 at 10iterations 4.859114 122.0531 at 20iterations 2.698902 63.78947 at 30iterations 1.496147 35.80008 at 40iterations 0.8240954 17.57268 at 50iterations 0.4518714 10.75818 at 60iterations 0.2484010 5.267575 at 70iterations 0.1359826 3.452842 at 80iterations 7.4364088E-02 1.550272 at 90iterations 4.0711366E-02 0.8210218 at 100iterations 2.2213090E-02 0.4794750 at 110iterations 1.2184715E-02 0.2589111 at 120iterations 6.6573522E-03 0.1443710 at 130iterations 3.6436988E-03 7.1941376E-02 at 140iterations 1.9963863E-03 3.9007366E-02 at 150iterations 1.1001545E-03 2.3340225E-02 at 160iterations 6.1348593E-04 1.4032841E-02 at 170iterations 3.4684423E-04 7.9241991E-03 at 180iterations finished qdiffx linear iterations at : 03:16:28 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 3.4684423E-04 7.9241991E-03 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 03:16:29 12.124u 0.218s 0:12.92 95.4% 0+0k 0+0io 0pf+0w