Mon Oct 10 19:32:44 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 Mon Oct 10 2011 at 19:32:44 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 = 3071 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5562674 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 0.5562674 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4999812 assigned positive charge : 460.6097 centred at (gu) : 90.47237 90.17825 89.71797 assigned negative charge : -461.1110 centred at (gu) : 90.50390 90.01107 89.61195 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6040 nv = 96 ne = 84 npr = 61981 no. pairs analyzed = 61981 no. exposed pairs = 3978 no. arc points = 27806 no. surface atoms = 1341 nbur = 1730 mkacc time = 0.1300000 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 = 1.540000 m= 238 mr = 3016 m= 0 mr = 11 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2824 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2044279E-09 9.4215624E-10 midg,1,midg; midg,igrid,midg -1.6836997E-09 1.6777042E-09 1,midg,midg; igrid,midg,midg 2.4317570E-10 -4.0543305E-10 gauss-seidel spectral radius is 0.9833397 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 19:32:45 rms-change max change #iterations 8.0750786E-02 13.15693 at 10iterations 5.5247527E-03 1.347014 at 20iterations 3.8697675E-04 6.1256409E-02 at 30iterations 2.8409551E-05 4.1799545E-03 at 40iterations 2.1956921E-06 2.9850006E-04 at 50iterations finished qdiffx linear iterations at : 19:32:47 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.1956921E-06 2.9850006E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 19:32:48 3.289u 0.165s 0:03.92 87.7% 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 Mon Oct 10 2011 at 19:32:48 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 = 3071 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.668802 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 1.668802 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4999812 assigned positive charge : 460.6097 centred at (gu) : 91.41598 90.53406 89.15318 assigned negative charge : -461.1110 centred at (gu) : 91.51151 90.03304 88.83563 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27806 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19892 mr = 44474 m= 2124 mr = 13247 m= 64 mr = 1058 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.4800000 number of dielectric boundary points 30211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 22538 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) : 0.5562674 object centre at (A) : 2.417001 2.094000 15.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0103753E-03 6.6603115E-03 midg,1,midg; midg,igrid,midg -1.9387141E-02 1.1256288E-02 1,midg,midg; igrid,midg,midg -1.4530522E-02 -1.4558667E-02 gauss-seidel spectral radius is 0.9982715 estimated iterations to convergence 191 setup time was (sec) 0.7700000 now iterating at: 19:32:49 rms-change max change #iterations 3.548402 169.1555 at 10iterations 1.508783 53.33870 at 20iterations 0.6401527 23.20638 at 30iterations 0.2715637 9.370496 at 40iterations 0.1161970 4.478215 at 50iterations 4.9155489E-02 1.939083 at 60iterations 2.0938171E-02 0.8948059 at 70iterations 8.9156814E-03 0.3055038 at 80iterations 3.8005307E-03 0.1372585 at 90iterations 1.6206511E-03 6.5395355E-02 at 100iterations 6.9038389E-04 2.3356438E-02 at 110iterations 2.9493368E-04 1.1366844E-02 at 120iterations finished qdiffx linear iterations at : 19:32:56 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 2.9493368E-04 1.1366844E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 19:32:56 7.370u 0.239s 0:08.08 94.0% 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 Mon Oct 10 2011 at 19:32:56 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 = 3071 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.503203 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): -29.58200 34.41600 ymin,ymax (A): -21.59900 25.78700 zmin,zma (A): -7.154000 39.02300 x,y,z range (A): 63.99800 47.38600 46.17700 scale (grids/A): 2.503203 object centre (A): 2.417001 2.094000 15.93450 number of atom coordinates read : 3071 total number of charged atoms : 2930 net assigned charge : -0.4999812 assigned positive charge : 460.6097 centred at (gu) : 92.12366 90.80097 88.72964 assigned negative charge : -461.1110 centred at (gu) : 92.26706 90.04929 88.25320 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 155494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27806 grid for indexing accessible points = 1.400000 m= 69167 mr = 109264 m= 19356 mr = 53640 m= 3218 mr = 14169 m= 268 mr = 2116 m= 6 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 1.130000 number of dielectric boundary points 68188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 23422 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) : 1.668802 object centre at (A) : 2.417001 2.094000 15.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1665241E-02 8.6819969E-02 midg,1,midg; midg,igrid,midg -0.2575340 0.1695577 1,midg,midg; igrid,midg,midg -0.3134699 -0.3617905 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.440000 now iterating at: 19:32:58 rms-change max change #iterations 9.067549 339.7752 at 10iterations 5.116094 143.3074 at 20iterations 2.875843 68.71397 at 30iterations 1.609917 33.63596 at 40iterations 0.9019973 19.86971 at 50iterations 0.5039620 9.983522 at 60iterations 0.2807003 6.153526 at 70iterations 0.1563869 3.031392 at 80iterations 8.6845517E-02 1.881948 at 90iterations 4.8295788E-02 0.9173737 at 100iterations 2.6872084E-02 0.5187168 at 110iterations 1.4898363E-02 0.2968874 at 120iterations 8.2677715E-03 0.1620712 at 130iterations 4.6055373E-03 9.0745926E-02 at 140iterations 2.5553773E-03 5.5433273E-02 at 150iterations 1.4196126E-03 2.7795672E-02 at 160iterations 7.8837841E-04 1.5384674E-02 at 170iterations 4.3649616E-04 9.7393990E-03 at 180iterations finished qdiffx linear iterations at : 19:33:08 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 4.3649616E-04 9.7393990E-03 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 19:33:09 11.962u 0.255s 0:13.04 93.6% 0+0k 0+0io 0pf+0w