Sun Oct 9 07:56:04 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 Sun Oct 9 2011 at 07:56:04 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 !!! WARNING: SEP 64 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7150317 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 0.7150317 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2024 net assigned charge : 7.525021 assigned positive charge : 322.3795 centred at (gu) : 89.79938 90.34939 90.17984 assigned negative charge : -314.8549 centred at (gu) : 89.66636 90.38149 90.22701 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7389 nv = 96 ne = 84 npr = 44147 no. pairs analyzed = 44147 no. exposed pairs = 2810 no. arc points = 19867 no. surface atoms = 938 nbur = 1225 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 483 mr = 3976 m= 8 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.1800000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1853 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0044671E-07 4.9827218E-08 midg,1,midg; midg,igrid,midg 8.9054872E-08 6.0970272E-08 1,midg,midg; igrid,midg,midg -3.6630430E-09 1.4789525E-07 gauss-seidel spectral radius is 0.9898159 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 07:56:05 rms-change max change #iterations 0.2098044 26.74155 at 10iterations 2.6306197E-02 3.334166 at 20iterations 3.3340235E-03 0.4603882 at 30iterations 4.1844742E-04 5.5374146E-02 at 40iterations 5.1942690E-05 6.9723129E-03 at 50iterations finished qdiffx linear iterations at : 07:56:08 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.1942690E-05 6.9723129E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:56:08 3.394u 0.172s 0:03.84 92.7% 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 Sun Oct 9 2011 at 07:56:08 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 !!! WARNING: SEP 64 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.145095 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 2.145095 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2024 net assigned charge : 7.525021 assigned positive charge : 322.3795 centred at (gu) : 89.39792 91.04758 90.53928 assigned negative charge : -314.8549 centred at (gu) : 88.99895 91.14417 90.68082 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19867 grid for indexing accessible points = 1.400000 m= 30411 mr = 53243 m= 5884 mr = 22690 m= 558 mr = 3797 m= 24 mr = 290 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2202 time to turn everything in is 0.3800000 number of dielectric boundary points 35213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16091 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) : 0.7150317 object centre at (A) : 7.085500 0.4899998 15.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0649467E-02 3.6042660E-02 midg,1,midg; midg,igrid,midg 3.2970879E-02 3.4572408E-02 1,midg,midg; igrid,midg,midg -1.4417092E-02 4.6380676E-02 gauss-seidel spectral radius is 0.9988679 estimated iterations to convergence 235 setup time was (sec) 0.5900000 now iterating at: 07:56:09 rms-change max change #iterations 4.751243 193.5771 at 10iterations 2.364767 75.32356 at 20iterations 1.178796 35.46626 at 30iterations 0.5918027 16.60822 at 40iterations 0.2961752 9.714884 at 50iterations 0.1476808 4.474823 at 60iterations 7.3989771E-02 2.101709 at 70iterations 3.7148360E-02 1.148880 at 80iterations 1.8542618E-02 0.5396080 at 90iterations 9.2703169E-03 0.2592392 at 100iterations 4.6594744E-03 0.1328175 at 110iterations 2.3335379E-03 6.8180084E-02 at 120iterations finished qdiffx linear iterations at : 07:56:16 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.3335379E-03 6.8180084E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 07:56:17 7.890u 0.221s 0:08.39 96.6% 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 Sun Oct 9 2011 at 07:56:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2163 !!! WARNING: SEP 64 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.217643 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): -16.22000 30.39100 ymin,ymax (A): -24.40400 25.38400 zmin,zma (A): -4.254000 35.01700 x,y,z range (A): 46.61100 49.78800 39.27100 scale (grids/A): 3.217643 object centre (A): 7.085500 0.4899998 15.38150 number of atom coordinates read : 2163 total number of charged atoms : 2024 net assigned charge : 7.525021 assigned positive charge : 322.3795 centred at (gu) : 89.09689 91.57141 90.80875 assigned negative charge : -314.8549 centred at (gu) : 88.49846 91.71615 91.02122 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 180559 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19867 grid for indexing accessible points = 1.400000 m= 94198 mr = 128805 m= 38575 mr = 77214 m= 11278 mr = 31544 m= 2293 mr = 8557 m= 321 mr = 1619 m= 27 mr = 227 m= 0 mr = 13 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 7083 time to turn everything in is 1.270000 number of dielectric boundary points 79272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 16192 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) : 2.145095 object centre at (A) : 7.085500 0.4899998 15.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6755584 0.3070171 midg,1,midg; midg,igrid,midg 0.2065810 0.3782353 1,midg,midg; igrid,midg,midg -5.7440847E-02 0.3072607 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 1.510000 now iterating at: 07:56:18 rms-change max change #iterations 10.48087 444.4185 at 10iterations 6.155226 124.7473 at 20iterations 3.602888 62.69106 at 30iterations 2.109589 40.62796 at 40iterations 1.234423 20.73283 at 50iterations 0.7204490 12.12056 at 60iterations 0.4214427 6.991493 at 70iterations 0.2466455 4.136654 at 80iterations 0.1439344 2.497704 at 90iterations 8.3993696E-02 1.682495 at 100iterations 4.9126729E-02 0.8150673 at 110iterations 2.8638450E-02 0.4652214 at 120iterations 1.6701363E-02 0.2687454 at 130iterations 9.7614666E-03 0.1645117 at 140iterations 5.7020313E-03 9.1125488E-02 at 150iterations 3.3272435E-03 5.4561615E-02 at 160iterations 1.9460727E-03 3.2396317E-02 at 170iterations 1.1377988E-03 2.0854950E-02 at 180iterations finished qdiffx linear iterations at : 07:56:30 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.1377988E-03 2.0854950E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 07:56:30 13.155u 0.220s 0:13.65 97.9% 0+0k 0+0io 0pf+0w