Mon Oct 10 14:00:19 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 Mon Oct 10 2011 at 14:00:19 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7486226 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): 8.634001 56.18800 ymin,ymax (A): -9.368000 36.26600 zmin,zma (A): -3.006000 43.86100 x,y,z range (A): 47.55400 45.63400 46.86700 scale (grids/A): 0.7486226 object centre (A): 32.41100 13.44900 20.42750 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 89.37707 90.71025 90.02725 assigned negative charge : -326.1720 centred at (gu) : 89.38364 90.77163 90.22903 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8169 nv = 96 ne = 84 npr = 43508 no. pairs analyzed = 43508 no. exposed pairs = 2716 no. arc points = 19237 no. surface atoms = 915 nbur = 1203 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 565 mr = 4530 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.1800000 number of dielectric boundary points 4112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1539 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8585 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0902664E-07 -3.8934024E-07 midg,1,midg; midg,igrid,midg -5.2546966E-08 -2.3932409E-07 1,midg,midg; igrid,midg,midg -1.4079377E-07 -1.2726349E-07 gauss-seidel spectral radius is 0.9907022 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 14:00:20 rms-change max change #iterations 0.2607552 30.89536 at 10iterations 3.6067758E-02 4.712751 at 20iterations 4.8654275E-03 0.6951790 at 30iterations 6.8371400E-04 8.3220482E-02 at 40iterations 9.2609000E-05 1.2256861E-02 at 50iterations finished qdiffx linear iterations at : 14:00:23 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 9.2609000E-05 1.2256861E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:00:23 3.392u 0.178s 0:04.36 81.6% 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 Mon Oct 10 2011 at 14:00:24 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.245868 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): 8.634001 56.18800 ymin,ymax (A): -9.368000 36.26600 zmin,zma (A): -3.006000 43.86100 x,y,z range (A): 47.55400 45.63400 46.86700 scale (grids/A): 2.245868 object centre (A): 32.41100 13.44900 20.42750 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 88.13100 92.13081 90.08156 assigned negative charge : -326.1720 centred at (gu) : 88.15092 92.31480 90.68712 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19237 grid for indexing accessible points = 1.400000 m= 34271 mr = 59342 m= 7366 mr = 26004 m= 834 mr = 5114 m= 31 mr = 451 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1445 time to turn everything in is 0.4300000 number of dielectric boundary points 37646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15768 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) : 0.7486226 object centre at (A) : 32.41100 13.44900 20.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5969997E-03 -0.1270997 midg,1,midg; midg,igrid,midg -3.6512695E-02 -4.5604859E-02 1,midg,midg; igrid,midg,midg 3.9404365E-03 2.0000078E-02 gauss-seidel spectral radius is 0.9989486 estimated iterations to convergence 244 setup time was (sec) 0.6400000 now iterating at: 14:00:24 rms-change max change #iterations 5.288397 210.3880 at 10iterations 2.700138 82.79426 at 20iterations 1.386551 41.66735 at 30iterations 0.7113857 18.79779 at 40iterations 0.3663213 11.21636 at 50iterations 0.1879317 5.410932 at 60iterations 9.6199155E-02 2.858786 at 70iterations 4.9487721E-02 1.439743 at 80iterations 2.5359653E-02 0.6994400 at 90iterations 1.3075256E-02 0.3691367 at 100iterations 6.7128562E-03 0.1947538 at 110iterations 3.4491895E-03 0.1051717 at 120iterations finished qdiffx linear iterations at : 14:00:32 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 3.4491895E-03 0.1051717 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 14:00:32 8.008u 0.236s 0:08.81 93.4% 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 14:00:32 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.368802 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): 8.634001 56.18800 ymin,ymax (A): -9.368000 36.26600 zmin,zma (A): -3.006000 43.86100 x,y,z range (A): 47.55400 45.63400 46.86700 scale (grids/A): 3.368802 object centre (A): 32.41100 13.44900 20.42750 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 87.19634 93.19602 90.12231 assigned negative charge : -326.1720 centred at (gu) : 87.22635 93.47235 91.03074 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 198015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19237 grid for indexing accessible points = 1.400000 m= 105234 mr = 142868 m= 44898 mr = 87083 m= 14248 mr = 37197 m= 3329 mr = 11288 m= 525 mr = 2589 m= 25 mr = 328 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 5226 time to turn everything in is 1.360000 number of dielectric boundary points 84914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15832 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) : 2.245868 object centre at (A) : 32.41100 13.44900 20.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1649636 -1.198341 midg,1,midg; midg,igrid,midg -0.3104767 -0.1963494 1,midg,midg; igrid,midg,midg 4.3075424E-02 0.1297913 gauss-seidel spectral radius is 0.9993244 estimated iterations to convergence 303 setup time was (sec) 1.620000 now iterating at: 14:00:34 rms-change max change #iterations 11.28413 306.4361 at 10iterations 6.677401 132.0136 at 20iterations 3.946558 70.37876 at 30iterations 2.333114 44.53217 at 40iterations 1.374399 27.75551 at 50iterations 0.8112912 14.60294 at 60iterations 0.4788068 7.822144 at 70iterations 0.2813732 4.738153 at 80iterations 0.1658449 2.606766 at 90iterations 9.7620919E-02 1.684845 at 100iterations 5.7549633E-02 0.9744110 at 110iterations 3.3808384E-02 0.6248169 at 120iterations 1.9917810E-02 0.3178545 at 130iterations 1.1687734E-02 0.1875234 at 140iterations 6.8982472E-03 0.1096344 at 150iterations 4.0647532E-03 6.4211369E-02 at 160iterations 2.3963132E-03 3.5076141E-02 at 170iterations 1.4097213E-03 2.3658752E-02 at 180iterations finished qdiffx linear iterations at : 14:00:47 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 1.4097213E-03 2.3658752E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.10000 DelPhi exited at 14:00:47 14.104u 0.327s 0:14.93 96.5% 0+0k 0+0io 0pf+0w