Sat Oct 15 14:14:59 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 Sat Oct 15 2011 at 14:14:59 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5233 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5056890 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): -18.75200 36.85900 ymin,ymax (A): -30.65000 31.41500 zmin,zma (A): -3.955000 66.44400 x,y,z range (A): 55.61100 62.06500 70.39900 scale (grids/A): 0.5056890 object centre (A): 9.053501 0.3824997 31.24450 number of atom coordinates read : 5233 total number of charged atoms : 4977 net assigned charge : 7.706049 assigned positive charge : 788.8214 centred at (gu) : 90.53011 90.97244 89.43456 assigned negative charge : -781.1205 centred at (gu) : 90.44799 91.00198 89.41472 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8418 nv = 96 ne = 84 npr = 106150 no. pairs analyzed = 106150 no. exposed pairs = 6532 no. arc points = 44951 no. surface atoms = 2206 nbur = 3027 mkacc time = 0.3100000 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 = 1.680000 m= 290 mr = 4363 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4341 ## 652 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 11200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8166474E-11 1.1460225E-10 midg,1,midg; midg,igrid,midg 1.2010513E-10 2.4113021E-11 1,midg,midg; igrid,midg,midg -8.8719261E-11 3.1534583E-10 gauss-seidel spectral radius is 0.9800345 estimated iterations to convergence 59 setup time was (sec) 0.8700000 now iterating at: 14:15:01 rms-change max change #iterations 6.9301613E-02 9.232632 at 10iterations 4.9796090E-03 0.9149933 at 20iterations 9.5191749E-04 0.1793213 at 30iterations 3.2964154E-04 4.4548035E-02 at 40iterations 1.2836506E-04 1.5014648E-02 at 50iterations finished qdiffx linear iterations at : 14:15:04 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.2836506E-04 1.5014648E-02 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 14:15:05 4.485u 0.300s 0:05.26 90.8% 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 Sat Oct 15 2011 at 14:15:05 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5233 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.517067 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): -18.75200 36.85900 ymin,ymax (A): -30.65000 31.41500 zmin,zma (A): -3.955000 66.44400 x,y,z range (A): 55.61100 62.06500 70.39900 scale (grids/A): 1.517067 object centre (A): 9.053501 0.3824997 31.24450 number of atom coordinates read : 5233 total number of charged atoms : 4977 net assigned charge : 7.706049 assigned positive charge : 788.8214 centred at (gu) : 91.58881 92.91550 88.30217 assigned negative charge : -781.1205 centred at (gu) : 91.34335 93.00575 88.24379 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 95719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27449 mr = 66233 m= 2404 mr = 17844 m= 62 mr = 965 m= 0 mr = 4 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 40588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 638 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 37248 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) : 0.5056890 object centre at (A) : 9.053501 0.3824997 31.24450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4959343E-03 2.0163162E-02 midg,1,midg; midg,igrid,midg -1.1530445E-03 -1.4553480E-02 1,midg,midg; igrid,midg,midg -1.3223611E-03 1.0768700E-02 gauss-seidel spectral radius is 0.9981108 estimated iterations to convergence 183 setup time was (sec) 1.180000 now iterating at: 14:15:06 rms-change max change #iterations 3.947449 162.6966 at 10iterations 1.612463 58.87254 at 20iterations 0.6627532 22.29292 at 30iterations 0.2720447 8.773656 at 40iterations 0.1118141 3.919170 at 50iterations 4.6094883E-02 1.500742 at 60iterations 1.9080425E-02 0.5929699 at 70iterations 8.0010584E-03 0.2585602 at 80iterations 3.4494202E-03 0.1302109 at 90iterations 1.5925384E-03 5.7762146E-02 at 100iterations 8.2831859E-04 2.8900146E-02 at 110iterations 4.9071357E-04 1.3448715E-02 at 120iterations finished qdiffx linear iterations at : 14:15:15 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 4.9071357E-04 1.3448715E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.17000 DelPhi exited at 14:15:16 10.170u 0.322s 0:10.80 97.1% 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 Sat Oct 15 2011 at 14:15:16 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5233 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.275600 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): -18.75200 36.85900 ymin,ymax (A): -30.65000 31.41500 zmin,zma (A): -3.955000 66.44400 x,y,z range (A): 55.61100 62.06500 70.39900 scale (grids/A): 2.275600 object centre (A): 9.053501 0.3824997 31.24450 number of atom coordinates read : 5233 total number of charged atoms : 4977 net assigned charge : 7.706049 assigned positive charge : 788.8214 centred at (gu) : 92.38282 94.37286 87.45293 assigned negative charge : -781.1205 centred at (gu) : 92.01521 94.50851 87.36557 start vw surface at 0.2400000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 223578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 99154 mr = 163037 m= 23973 mr = 76763 m= 3368 mr = 16678 m= 184 mr = 1927 m= 5 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 91804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 39696 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) : 1.517067 object centre at (A) : 9.053501 0.3824997 31.24450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1702486 0.3580271 midg,1,midg; midg,igrid,midg -0.1121016 -0.3738850 1,midg,midg; igrid,midg,midg -2.1960456E-02 0.1555284 gauss-seidel spectral radius is 0.9991719 estimated iterations to convergence 274 setup time was (sec) 2.470000 now iterating at: 14:15:18 rms-change max change #iterations 10.71978 263.1629 at 10iterations 6.173111 154.3623 at 20iterations 3.518036 71.74013 at 30iterations 2.000585 43.91259 at 40iterations 1.132825 25.65284 at 50iterations 0.6380024 13.48239 at 60iterations 0.3596009 7.568566 at 70iterations 0.2018314 4.171098 at 80iterations 0.1130209 2.468676 at 90iterations 6.3332386E-02 1.341492 at 100iterations 3.5484064E-02 0.6884050 at 110iterations 1.9810153E-02 0.3738117 at 120iterations 1.1098375E-02 0.2109451 at 130iterations 6.2160427E-03 0.1248198 at 140iterations 3.4902620E-03 6.8922043E-02 at 150iterations 1.9708036E-03 3.6148071E-02 at 160iterations 1.1319217E-03 2.1489620E-02 at 170iterations 6.6294271E-04 1.2264252E-02 at 180iterations finished qdiffx linear iterations at : 14:15:33 total time elapsed so far: 17.52000 # loops : 180 mean,max change (kT/e) : 6.6294271E-04 1.2264252E-02 energy calculations done at 17.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.69000 DelPhi exited at 14:15:34 17.695u 0.342s 0:18.32 98.4% 0+0k 0+0io 0pf+0w