Tue Oct 11 03:24:16 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 03:24:16 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 = 5575 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4989768 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 0.4989768 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5412 net assigned charge : 4.3481588E-05 assigned positive charge : 862.5767 centred at (gu) : 90.47339 90.26245 88.41256 assigned negative charge : -862.5847 centred at (gu) : 90.49040 90.23683 88.51906 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8818 nv = 96 ne = 84 npr = 109610 no. pairs analyzed = 109610 no. exposed pairs = 7238 no. arc points = 50230 no. surface atoms = 2398 nbur = 3177 mkacc time = 0.2300000 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 = 1.708000 m= 317 mr = 4432 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4749 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11798 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0029848E-10 -1.3437131E-10 midg,1,midg; midg,igrid,midg -4.8219428E-11 4.7820376E-11 1,midg,midg; igrid,midg,midg 2.4985193E-11 -4.0452801E-11 gauss-seidel spectral radius is 0.9795284 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 03:24:17 rms-change max change #iterations 6.6238694E-02 9.295431 at 10iterations 3.5996325E-03 0.5163460 at 20iterations 3.0728825E-04 4.5185089E-02 at 30iterations 6.9867114E-05 9.1190338E-03 at 40iterations 2.1874794E-05 2.9003620E-03 at 50iterations finished qdiffx linear iterations at : 03:24:20 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.1874794E-05 2.9003620E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 03:24:20 3.552u 0.139s 0:04.18 88.0% 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 03:24:21 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 = 5575 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.496930 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 1.496930 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5412 net assigned charge : 4.3481588E-05 assigned positive charge : 862.5767 centred at (gu) : 91.41811 90.78539 85.23605 assigned negative charge : -862.5847 centred at (gu) : 91.47092 90.71036 85.55699 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 100505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50230 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28712 mr = 68248 m= 2254 mr = 18751 m= 46 mr = 840 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1021 time to turn everything in is 0.7100000 number of dielectric boundary points 43678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 587 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 40250 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) : 0.4989768 object centre at (A) : 19.20400 -9.774001 18.73600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3148517E-02 5.2028778E-03 midg,1,midg; midg,igrid,midg -1.2193450E-02 -1.7095549E-02 1,midg,midg; igrid,midg,midg -1.5627937E-03 -4.7871177E-03 gauss-seidel spectral radius is 0.9980924 estimated iterations to convergence 182 setup time was (sec) 0.9900000 now iterating at: 03:24:22 rms-change max change #iterations 4.023606 164.7697 at 10iterations 1.632249 55.12254 at 20iterations 0.6676991 20.25073 at 30iterations 0.2718520 8.516589 at 40iterations 0.1112447 3.588615 at 50iterations 4.5350298E-02 1.338829 at 60iterations 1.8514192E-02 0.6687546 at 70iterations 7.5810566E-03 0.2177658 at 80iterations 3.1075191E-03 0.1083260 at 90iterations 1.2744453E-03 3.7261963E-02 at 100iterations 5.2583253E-04 1.6822815E-02 at 110iterations 2.1850877E-04 6.5350533E-03 at 120iterations finished qdiffx linear iterations at : 03:24:28 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.1850877E-04 6.5350533E-03 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 03:24:29 7.674u 0.243s 0:08.48 93.2% 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 Tue Oct 11 2011 at 03:24:29 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 = 5575 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.245396 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 2.245396 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5412 net assigned charge : 4.3481588E-05 assigned positive charge : 862.5767 centred at (gu) : 92.12685 91.17764 82.85321 assigned negative charge : -862.5847 centred at (gu) : 92.20620 91.06542 83.33551 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 234429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50230 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 104055 mr = 168039 m= 24758 mr = 80545 m= 2956 mr = 17319 m= 122 mr = 1586 m= 0 mr = 24 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 3582 time to turn everything in is 1.690000 number of dielectric boundary points 98807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 43122 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) : 1.496930 object centre at (A) : 19.20400 -9.774001 18.73600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1941224 0.1324157 midg,1,midg; midg,igrid,midg -0.3088985 -0.4344579 1,midg,midg; igrid,midg,midg -2.0566983E-02 -3.7435908E-02 gauss-seidel spectral radius is 0.9991751 estimated iterations to convergence 275 setup time was (sec) 2.020000 now iterating at: 03:24:31 rms-change max change #iterations 11.14185 263.6513 at 10iterations 6.449916 175.5977 at 20iterations 3.702430 79.34699 at 30iterations 2.116884 42.41778 at 40iterations 1.202568 25.12255 at 50iterations 0.6805881 12.93619 at 60iterations 0.3836859 8.151911 at 70iterations 0.2164318 4.406132 at 80iterations 0.1219054 2.374062 at 90iterations 6.8345621E-02 1.307532 at 100iterations 3.8368091E-02 0.7232533 at 110iterations 2.1507336E-02 0.3973751 at 120iterations 1.2005542E-02 0.2290115 at 130iterations 6.7323418E-03 0.1227684 at 140iterations 3.7596100E-03 7.1525574E-02 at 150iterations 2.1028165E-03 3.9381027E-02 at 160iterations 1.1776892E-03 1.9866943E-02 at 170iterations 6.5783662E-04 1.1606216E-02 at 180iterations finished qdiffx linear iterations at : 03:24:42 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 6.5783662E-04 1.1606216E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 03:24:43 13.093u 0.242s 0:13.78 96.7% 0+0k 0+0io 0pf+0w