Sun Oct 9 06:04:17 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 06:04:18 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2026 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6279435 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): 11.67400 68.36700 ymin,ymax (A): -26.39100 26.87100 zmin,zma (A): -5.854000 36.34300 x,y,z range (A): 56.69300 53.26200 42.19700 scale (grids/A): 0.6279435 object centre (A): 40.02050 0.2399998 15.24450 number of atom coordinates read : 2026 total number of charged atoms : 1879 net assigned charge : -11.56599 assigned positive charge : 313.7565 centred at (gu) : 90.98735 89.35646 90.66057 assigned negative charge : -325.3229 centred at (gu) : 91.00338 89.06558 90.41779 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5508 nv = 96 ne = 84 npr = 39507 no. pairs analyzed = 39507 no. exposed pairs = 2886 no. arc points = 20378 no. surface atoms = 964 nbur = 1062 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 2667 m= 0 mr = 26 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2400000 number of dielectric boundary points 3100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6403 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5261368E-08 5.6448410E-09 midg,1,midg; midg,igrid,midg -3.7660239E-08 6.8207826E-09 1,midg,midg; igrid,midg,midg -8.6406500E-09 -1.5844325E-08 gauss-seidel spectral radius is 0.9868255 estimated iterations to convergence 71 setup time was (sec) 0.4900000 now iterating at: 06:04:18 rms-change max change #iterations 0.1201957 20.77682 at 10iterations 1.1254488E-02 1.744761 at 20iterations 1.0737446E-03 0.1877441 at 30iterations 1.0869992E-04 1.8467903E-02 at 40iterations 1.2266676E-05 2.0484924E-03 at 50iterations finished qdiffx linear iterations at : 06:04:21 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.2266676E-05 2.0484924E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:04:21 3.374u 0.207s 0:03.84 92.9% 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 06:04:21 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2026 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.883831 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): 11.67400 68.36700 ymin,ymax (A): -26.39100 26.87100 zmin,zma (A): -5.854000 36.34300 x,y,z range (A): 56.69300 53.26200 42.19700 scale (grids/A): 1.883831 object centre (A): 40.02050 0.2399998 15.24450 number of atom coordinates read : 2026 total number of charged atoms : 1879 net assigned charge : -11.56599 assigned positive charge : 313.7565 centred at (gu) : 92.96175 88.06925 91.98146 assigned negative charge : -325.3229 centred at (gu) : 93.00998 87.19673 91.25327 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20378 grid for indexing accessible points = 1.400000 m= 20002 mr = 37914 m= 2917 mr = 13858 m= 157 mr = 1660 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 879 time to turn everything in is 0.4400000 number of dielectric boundary points 28549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14743 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) : 0.6279435 object centre at (A) : 40.02050 0.2399998 15.24450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0069795E-02 4.8707752E-03 midg,1,midg; midg,igrid,midg -5.8951970E-02 3.8382590E-02 1,midg,midg; igrid,midg,midg -3.6621179E-02 -7.1135737E-02 gauss-seidel spectral radius is 0.9985599 estimated iterations to convergence 209 setup time was (sec) 0.7300000 now iterating at: 06:04:22 rms-change max change #iterations 3.817324 184.6566 at 10iterations 1.735731 77.51570 at 20iterations 0.7915806 27.06685 at 30iterations 0.3617897 15.40117 at 40iterations 0.1661471 5.742967 at 50iterations 7.5809158E-02 2.718183 at 60iterations 3.4757804E-02 1.269421 at 70iterations 1.5819229E-02 0.5664067 at 80iterations 7.2755860E-03 0.2752819 at 90iterations 3.3189508E-03 0.1125870 at 100iterations 1.5300348E-03 5.2765846E-02 at 110iterations 7.0564391E-04 2.5181770E-02 at 120iterations finished qdiffx linear iterations at : 06:04:29 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 7.0564391E-04 2.5181770E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 06:04:30 7.582u 0.247s 0:08.08 96.7% 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 06:04:30 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2026 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 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: 2.825746 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): 11.67400 68.36700 ymin,ymax (A): -26.39100 26.87100 zmin,zma (A): -5.854000 36.34300 x,y,z range (A): 56.69300 53.26200 42.19700 scale (grids/A): 2.825746 object centre (A): 40.02050 0.2399998 15.24450 number of atom coordinates read : 2026 total number of charged atoms : 1879 net assigned charge : -11.56599 assigned positive charge : 313.7565 centred at (gu) : 94.44259 87.10372 92.97198 assigned negative charge : -325.3229 centred at (gu) : 94.51501 85.79505 91.87996 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 135837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20378 grid for indexing accessible points = 1.400000 m= 64813 mr = 92259 m= 22584 mr = 51048 m= 5120 mr = 17382 m= 634 mr = 3606 m= 34 mr = 351 m= 0 mr = 13 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2777 time to turn everything in is 1.070000 number of dielectric boundary points 64363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 15031 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) : 1.883831 object centre at (A) : 40.02050 0.2399998 15.24450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2908402 5.1024448E-02 midg,1,midg; midg,igrid,midg -0.8419713 0.3724316 1,midg,midg; igrid,midg,midg -0.4777251 -0.9757358 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 1.400000 now iterating at: 06:04:31 rms-change max change #iterations 9.005723 355.6332 at 10iterations 5.226032 133.4436 at 20iterations 3.003437 64.74220 at 30iterations 1.720169 39.71169 at 40iterations 0.9836040 23.16207 at 50iterations 0.5638785 12.25990 at 60iterations 0.3200066 6.642475 at 70iterations 0.1822309 3.789501 at 80iterations 0.1040508 2.594673 at 90iterations 5.9159797E-02 1.220833 at 100iterations 3.3633161E-02 0.7109063 at 110iterations 1.9161871E-02 0.3889751 at 120iterations 1.0892577E-02 0.2220154 at 130iterations 6.2372447E-03 0.1226730 at 140iterations 3.5634397E-03 7.1729660E-02 at 150iterations 2.0577216E-03 4.5762062E-02 at 160iterations 1.1962064E-03 2.8802872E-02 at 170iterations 7.0306356E-04 1.7758608E-02 at 180iterations finished qdiffx linear iterations at : 06:04:42 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 7.0306356E-04 1.7758608E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 06:04:42 12.142u 0.246s 0:12.68 97.6% 0+0k 0+0io 0pf+0w