Thu Jan 19 13:33:08 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 13:33:12 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4319025 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 0.4319025 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388949 assigned positive charge : 1017.237 centred at (gu) : 88.61485 89.94763 91.92900 assigned negative charge : -1025.636 centred at (gu) : 88.64067 89.90337 91.97630 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7684 nv = 96 ne = 84 npr = 133777 no. pairs analyzed = 133777 no. exposed pairs = 8887 no. arc points = 60986 no. surface atoms = 2979 nbur = 3757 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 = 1.932000 m= 205 mr = 3690 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5022 ## 1016 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5543358E-13 -9.3798606E-12 midg,1,midg; midg,igrid,midg -5.0094030E-12 1.1833190E-12 1,midg,midg; igrid,midg,midg -4.5550996E-14 -2.3885921E-12 gauss-seidel spectral radius is 0.9728017 estimated iterations to convergence 51 setup time was (sec) 0.6200000 now iterating at: 13:33:16 rms-change max change #iterations 3.1882018E-02 5.940651 at 10iterations 2.5665981E-03 0.4192162 at 20iterations 8.6575345E-04 0.1441135 at 30iterations 3.2152981E-04 5.2591324E-02 at 40iterations 1.1968770E-04 1.9416809E-02 at 50iterations finished qdiffx linear iterations at : 13:33:25 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 1.1968770E-04 1.9416809E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 13:33:26 3.774u 0.189s 0:14.23 27.7% 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 Thu Jan 19 2012 at 13:33:28 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 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: 1.295708 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 1.295708 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388949 assigned positive charge : 1017.237 centred at (gu) : 85.84277 89.84032 95.78461 assigned negative charge : -1025.636 centred at (gu) : 85.92162 89.70952 95.92827 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 90285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 21181 mr = 59993 m= 1014 mr = 12676 m= 9 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 313 time to turn everything in is 0.4600000 number of dielectric boundary points 39576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1034 ## 39 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45850 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) : 0.4319025 object centre at (A) : 29.33800 -56.97800 26.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6560490E-04 4.1498812E-03 midg,1,midg; midg,igrid,midg -2.9915003E-03 -7.2384457E-04 1,midg,midg; igrid,midg,midg -9.9747360E-04 -1.4882296E-03 gauss-seidel spectral radius is 0.9974369 estimated iterations to convergence 157 setup time was (sec) 0.6800000 now iterating at: 13:33:33 rms-change max change #iterations 3.078684 137.8475 at 10iterations 1.086532 36.74278 at 20iterations 0.3866394 13.41792 at 30iterations 0.1367721 4.598419 at 40iterations 4.8574820E-02 1.743402 at 50iterations 1.7513514E-02 0.6344795 at 60iterations 6.4550503E-03 0.2479992 at 70iterations 2.5663872E-03 9.7141266E-02 at 80iterations 1.2143619E-03 4.3794632E-02 at 90iterations 7.0140540E-04 2.5554657E-02 at 100iterations 4.5507911E-04 1.5777588E-02 at 110iterations 3.0784582E-04 1.0045171E-02 at 120iterations finished qdiffx linear iterations at : 13:33:51 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 3.0784582E-04 1.0045171E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 13:33:51 8.073u 0.226s 0:23.30 35.5% 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 Thu Jan 19 2012 at 13:33:52 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 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: 1.943561 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 1.943561 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388949 assigned positive charge : 1017.237 centred at (gu) : 83.76360 89.75999 98.67640 assigned negative charge : -1025.636 centred at (gu) : 83.88228 89.56418 98.89238 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 211659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 82620 mr = 149780 m= 14966 mr = 61062 m= 1060 mr = 9468 m= 27 mr = 434 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.070000 number of dielectric boundary points 89588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 51993 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) : 1.295708 object centre at (A) : 29.33800 -56.97800 26.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9906243E-02 0.5162121 midg,1,midg; midg,igrid,midg -9.8486535E-02 -2.5929840E-02 1,midg,midg; igrid,midg,midg 2.7187006E-03 -4.1440573E-02 gauss-seidel spectral radius is 0.9989914 estimated iterations to convergence 249 setup time was (sec) 1.330000 now iterating at: 13:33:53 rms-change max change #iterations 9.435746 299.2244 at 10iterations 5.140534 130.6563 at 20iterations 2.766891 64.22793 at 30iterations 1.482538 36.76758 at 40iterations 0.7903550 22.88540 at 50iterations 0.4208636 10.24767 at 60iterations 0.2230236 4.941355 at 70iterations 0.1178553 2.578629 at 80iterations 6.2241148E-02 1.398180 at 90iterations 3.2785211E-02 0.6998763 at 100iterations 1.7298490E-02 0.3588238 at 110iterations 9.1109890E-03 0.1999512 at 120iterations 4.8045372E-03 0.1076698 at 130iterations 2.5433637E-03 5.4208755E-02 at 140iterations 1.3546941E-03 2.6779175E-02 at 150iterations 7.3485327E-04 1.5949249E-02 at 160iterations 4.0985711E-04 8.3961487E-03 at 170iterations 2.3950050E-04 5.3482056E-03 at 180iterations finished qdiffx linear iterations at : 13:34:22 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 2.3950050E-04 5.3482056E-03 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 13:34:22 13.356u 0.221s 0:30.78 44.0% 0+0k 0+0io 0pf+0w