Sun Oct 9 11:44:20 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 11:44:21 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6527079 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 0.6527079 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.514011 assigned positive charge : 408.7340 centred at (gu) : 90.76109 90.22046 90.95095 assigned negative charge : -405.2217 centred at (gu) : 90.81497 90.17364 90.94310 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 50366 no. pairs analyzed = 50366 no. exposed pairs = 3802 no. arc points = 27448 no. surface atoms = 1268 nbur = 1435 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 570 mr = 4183 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2579 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9762434E-09 1.0574122E-08 midg,1,midg; midg,igrid,midg -6.3373207E-10 1.6035550E-08 1,midg,midg; igrid,midg,midg 1.4086281E-08 -2.3195650E-09 gauss-seidel spectral radius is 0.9878697 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 11:44:21 rms-change max change #iterations 0.1636552 23.41904 at 10iterations 1.6899269E-02 2.253422 at 20iterations 1.7266796E-03 0.2268562 at 30iterations 1.8593356E-04 2.6226997E-02 at 40iterations 2.7569624E-05 5.0106049E-03 at 50iterations finished qdiffx linear iterations at : 11:44:24 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.7569624E-05 5.0106049E-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) 3.400000 DelPhi exited at 11:44:24 3.403u 0.181s 0:03.87 92.5% 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 Sun Oct 9 2011 at 11:44:24 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.958124 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 1.958124 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.514011 assigned positive charge : 408.7340 centred at (gu) : 92.28218 90.66062 92.85175 assigned negative charge : -405.2217 centred at (gu) : 92.44491 90.52077 92.82915 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27448 grid for indexing accessible points = 1.400000 m= 33290 mr = 58164 m= 6594 mr = 23744 m= 524 mr = 4253 m= 11 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.4300000 number of dielectric boundary points 42038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20862 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) : 0.6527079 object centre at (A) : 21.30950 34.57100 31.91900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2495804E-03 3.0621689E-02 midg,1,midg; midg,igrid,midg -3.5103005E-03 2.9791927E-02 1,midg,midg; igrid,midg,midg 2.2527487E-04 -9.0288054E-03 gauss-seidel spectral radius is 0.9987525 estimated iterations to convergence 224 setup time was (sec) 0.6500000 now iterating at: 11:44:25 rms-change max change #iterations 4.628899 197.4286 at 10iterations 2.237586 82.23815 at 20iterations 1.079153 36.59192 at 30iterations 0.5228823 15.72403 at 40iterations 0.2529669 7.911743 at 50iterations 0.1219124 3.768619 at 60iterations 5.8903553E-02 1.690876 at 70iterations 2.8509840E-02 0.8106508 at 80iterations 1.3755659E-02 0.4018536 at 90iterations 6.6633513E-03 0.2000999 at 100iterations 3.2248290E-03 9.5682144E-02 at 110iterations 1.5609491E-03 4.3625832E-02 at 120iterations finished qdiffx linear iterations at : 11:44:32 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.5609491E-03 4.3625832E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 11:44:33 8.016u 0.193s 0:08.48 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 11:44:33 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.937186 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 2.937186 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.514011 assigned positive charge : 408.7340 centred at (gu) : 93.42318 90.99075 94.27737 assigned negative charge : -405.2217 centred at (gu) : 93.66727 90.78114 94.24358 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 202809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27448 grid for indexing accessible points = 1.400000 m= 102791 mr = 141753 m= 42060 mr = 81640 m= 12534 mr = 33375 m= 2176 mr = 9432 m= 168 mr = 1478 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 1162 time to turn everything in is 1.140000 number of dielectric boundary points 94782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 21128 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) : 1.958124 object centre at (A) : 21.30950 34.57100 31.91900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1261311E-03 0.3737534 midg,1,midg; midg,igrid,midg 6.9724028E-03 0.3368327 1,midg,midg; igrid,midg,midg -5.1967572E-02 -4.8598912E-02 gauss-seidel spectral radius is 0.9993185 estimated iterations to convergence 302 setup time was (sec) 1.390000 now iterating at: 11:44:35 rms-change max change #iterations 10.96299 470.6284 at 10iterations 6.677740 177.9325 at 20iterations 4.044040 92.52858 at 30iterations 2.427661 53.64344 at 40iterations 1.450957 28.44318 at 50iterations 0.8677267 19.10935 at 60iterations 0.5160466 9.946404 at 70iterations 0.3063827 5.412046 at 80iterations 0.1814134 3.531090 at 90iterations 0.1069467 2.059436 at 100iterations 6.3319862E-02 1.151015 at 110iterations 3.7391160E-02 0.6485519 at 120iterations 2.2033649E-02 0.3670349 at 130iterations 1.2997868E-02 0.2240219 at 140iterations 7.6608919E-03 0.1389790 at 150iterations 4.5261127E-03 7.4298859E-02 at 160iterations 2.6760846E-03 5.2001953E-02 at 170iterations 1.5852305E-03 2.5033236E-02 at 180iterations finished qdiffx linear iterations at : 11:44:46 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 1.5852305E-03 2.5033236E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 11:44:47 13.232u 0.213s 0:13.75 97.7% 0+0k 0+0io 0pf+0w