Tue Oct 11 06:54:17 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 06:54:17 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 0.6000438 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 0.6000438 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 435.4585 centred at (gu) : 89.42862 89.90242 89.49732 assigned negative charge : -441.9590 centred at (gu) : 89.39278 90.16650 89.49780 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 63870 no. pairs analyzed = 63870 no. exposed pairs = 3722 no. arc points = 25843 no. surface atoms = 1263 nbur = 1737 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3728 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3800000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2528 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0766192E-09 -2.5034148E-09 midg,1,midg; midg,igrid,midg 8.0686773E-09 -1.3794359E-08 1,midg,midg; igrid,midg,midg -4.8563757E-09 -1.1468537E-09 gauss-seidel spectral radius is 0.9856573 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 06:54:18 rms-change max change #iterations 0.1186033 18.53494 at 10iterations 1.0196814E-02 1.690444 at 20iterations 8.8164868E-04 0.1200218 at 30iterations 7.8338613E-05 9.5901489E-03 at 40iterations 7.2532735E-06 1.0147095E-03 at 50iterations finished qdiffx linear iterations at : 06:54:21 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 7.2532735E-06 1.0147095E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 06:54:21 4.146u 0.269s 0:04.86 90.5% 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 06:54:22 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 1.800131 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 1.800131 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 435.4585 centred at (gu) : 88.28541 89.70686 88.49141 assigned negative charge : -441.9590 centred at (gu) : 88.17815 90.49911 88.49297 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 grid for indexing accessible points = 1.400000 m= 26013 mr = 51738 m= 3776 mr = 18407 m= 159 mr = 2218 m= 0 mr = 36 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 33070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22213 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) : 0.6000438 object centre at (A) : 14.36050 48.13600 -44.65650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0612164E-02 1.6402327E-02 midg,1,midg; midg,igrid,midg 3.0678054E-03 -3.6262408E-02 1,midg,midg; igrid,midg,midg -4.0826052E-02 -3.9636433E-02 gauss-seidel spectral radius is 0.9985145 estimated iterations to convergence 206 setup time was (sec) 0.9800000 now iterating at: 06:54:23 rms-change max change #iterations 4.081035 173.5148 at 10iterations 1.825888 61.66537 at 20iterations 0.8313913 29.48000 at 30iterations 0.3755468 13.26051 at 40iterations 0.1707870 5.591851 at 50iterations 7.7450849E-02 2.716373 at 60iterations 3.5082992E-02 1.199745 at 70iterations 1.5897330E-02 0.5037479 at 80iterations 7.1899728E-03 0.2293048 at 90iterations 3.2585743E-03 9.7183228E-02 at 100iterations 1.4828570E-03 4.6823502E-02 at 110iterations 6.7138957E-04 2.2148132E-02 at 120iterations finished qdiffx linear iterations at : 06:54:31 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 6.7138957E-04 2.2148132E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 06:54:32 9.598u 0.314s 0:10.42 95.0% 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 06:54:32 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 2.700197 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 2.700197 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 435.4585 centred at (gu) : 87.42782 89.56019 87.73679 assigned negative charge : -441.9590 centred at (gu) : 87.26687 90.74844 87.73938 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 174984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 grid for indexing accessible points = 1.400000 m= 84745 mr = 125954 m= 29449 mr = 67911 m= 6588 mr = 22972 m= 777 mr = 4685 m= 28 mr = 463 m= 0 mr = 9 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 74577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 22708 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) : 1.800131 object centre at (A) : 14.36050 48.13600 -44.65650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1493734 0.3044715 midg,1,midg; midg,igrid,midg 4.7204640E-02 -0.3220311 1,midg,midg; igrid,midg,midg -0.4556507 -0.5941815 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 2.080000 now iterating at: 06:54:34 rms-change max change #iterations 10.03637 343.3159 at 10iterations 5.890174 198.7395 at 20iterations 3.419681 67.44099 at 30iterations 1.980069 38.06002 at 40iterations 1.139488 25.90096 at 50iterations 0.6545433 13.06651 at 60iterations 0.3748133 7.772953 at 70iterations 0.2150756 4.522606 at 80iterations 0.1226805 2.400013 at 90iterations 7.0275724E-02 1.296349 at 100iterations 3.9991263E-02 0.7735176 at 110iterations 2.2882314E-02 0.4357224 at 120iterations 1.3040181E-02 0.2301216 at 130iterations 7.4380455E-03 0.1266060 at 140iterations 4.2457115E-03 8.6372375E-02 at 150iterations 2.4201304E-03 4.0845871E-02 at 160iterations 1.3795170E-03 2.5438309E-02 at 170iterations 7.8697776E-04 1.4839172E-02 at 180iterations finished qdiffx linear iterations at : 06:54:48 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 7.8697776E-04 1.4839172E-02 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.31000 DelPhi exited at 06:54:49 16.310u 0.298s 0:16.97 97.8% 0+0k 0+0io 0pf+0w