Thu Jan 19 13:32:41 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:46 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4225920 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 0.4225920 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1032.429 centred at (gu) : 91.20169 89.91972 91.54321 assigned negative charge : -1040.229 centred at (gu) : 91.17817 89.96741 91.60839 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 136208 no. pairs analyzed = 136208 no. exposed pairs = 8927 no. arc points = 60881 no. surface atoms = 2995 nbur = 3834 mkacc time = 0.2300000 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 = 1.988000 m= 195 mr = 3495 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4974 ## 1085 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10115 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9240277E-13 -5.8405555E-12 midg,1,midg; midg,igrid,midg 9.7134258E-13 -2.7906674E-12 1,midg,midg; igrid,midg,midg -1.2991915E-12 8.4183098E-15 gauss-seidel spectral radius is 0.9716048 estimated iterations to convergence 50 setup time was (sec) 0.6200000 now iterating at: 13:32:49 rms-change max change #iterations 2.9034650E-02 4.650764 at 10iterations 2.5852742E-03 0.4330978 at 20iterations 9.8321820E-04 0.1734505 at 30iterations 4.0085241E-04 7.1429253E-02 at 40iterations 1.6380360E-04 2.9241562E-02 at 50iterations finished qdiffx linear iterations at : 13:32:59 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 1.6380360E-04 2.9241562E-02 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 13:33:00 3.817u 0.177s 0:15.10 26.3% 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 Thu Jan 19 2012 at 13:33:02 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.267776 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 1.267776 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1032.429 centred at (gu) : 93.60291 89.75761 94.62797 assigned negative charge : -1040.229 centred at (gu) : 93.53435 89.90180 94.82458 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 86581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60881 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19960 mr = 57311 m= 940 mr = 11755 m= 5 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4600000 number of dielectric boundary points 38272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1120 ## 45 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45847 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) : 0.4225920 object centre at (A) : -29.26550 56.88600 -0.8210011 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1048919E-03 -8.7293116E-03 midg,1,midg; midg,igrid,midg -1.1034572E-03 -6.8579474E-03 1,midg,midg; igrid,midg,midg -2.3513197E-04 -1.0949391E-03 gauss-seidel spectral radius is 0.9973080 estimated iterations to convergence 154 setup time was (sec) 0.6900000 now iterating at: 13:33:07 rms-change max change #iterations 2.940046 124.3052 at 10iterations 1.017819 36.97086 at 20iterations 0.3510861 14.43533 at 30iterations 0.1213736 4.318014 at 40iterations 4.2107932E-02 1.518695 at 50iterations 1.4786431E-02 0.5380840 at 60iterations 5.4178457E-03 0.2315354 at 70iterations 2.2780690E-03 8.2160950E-02 at 80iterations 1.2281303E-03 4.9698830E-02 at 90iterations 8.0266647E-04 2.9568672E-02 at 100iterations 5.6799955E-04 2.1011353E-02 at 110iterations 4.1014477E-04 1.5149117E-02 at 120iterations finished qdiffx linear iterations at : 13:33:28 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 4.1014477E-04 1.5149117E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 13:33:29 8.148u 0.213s 0:26.83 31.1% 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 Thu Jan 19 2012 at 13:33:30 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.901664 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 1.901664 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1032.429 centred at (gu) : 95.40378 89.63566 96.94144 assigned negative charge : -1040.229 centred at (gu) : 95.30148 89.85246 97.23689 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 203682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60881 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 77988 mr = 143697 m= 13643 mr = 57273 m= 868 mr = 8458 m= 16 mr = 265 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 192 time to turn everything in is 1.050000 number of dielectric boundary points 86505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 52458 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) : 1.267776 object centre at (A) : -29.26550 56.88600 -0.8210011 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8378228E-02 -0.1321646 midg,1,midg; midg,igrid,midg -1.6540891E-02 -0.2377741 1,midg,midg; igrid,midg,midg -6.1103753E-03 -3.9289449E-03 gauss-seidel spectral radius is 0.9989500 estimated iterations to convergence 244 setup time was (sec) 1.290000 now iterating at: 13:33:31 rms-change max change #iterations 9.228764 258.5914 at 10iterations 4.964512 134.0790 at 20iterations 2.649038 74.19587 at 30iterations 1.401594 35.73080 at 40iterations 0.7365791 19.50099 at 50iterations 0.3866505 9.247897 at 60iterations 0.2024320 5.113197 at 70iterations 0.1055831 2.470753 at 80iterations 5.5033568E-02 1.188503 at 90iterations 2.8604744E-02 0.5853949 at 100iterations 1.4876631E-02 0.3477249 at 110iterations 7.7646854E-03 0.1739149 at 120iterations 4.0558162E-03 9.5851898E-02 at 130iterations 2.1450813E-03 4.3933868E-02 at 140iterations 1.1578634E-03 2.4705172E-02 at 150iterations 6.5423641E-04 1.4852524E-02 at 160iterations 3.9731120E-04 9.3269348E-03 at 170iterations 2.6267141E-04 5.9623718E-03 at 180iterations finished qdiffx linear iterations at : 13:34:04 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 2.6267141E-04 5.9623718E-03 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.15000 DelPhi exited at 13:34:05 14.150u 0.270s 0:34.70 41.5% 0+0k 0+0io 0pf+0w