Mon Oct 10 14:00:21 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 14:00:22 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 = 1966 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: 0.6422979 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 0.6422979 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.14947 92.56746 90.18553 assigned negative charge : -282.5023 centred at (gu) : 90.23695 92.66750 90.12657 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 39967 no. pairs analyzed = 39967 no. exposed pairs = 2504 no. arc points = 17553 no. surface atoms = 856 nbur = 1110 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3110 m= 0 mr = 50 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5806408E-09 1.3770076E-08 midg,1,midg; midg,igrid,midg 9.8642881E-09 -2.3258016E-09 1,midg,midg; igrid,midg,midg 1.5267727E-08 6.0069831E-11 gauss-seidel spectral radius is 0.9873868 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 14:00:22 rms-change max change #iterations 0.1255817 22.34842 at 10iterations 1.2682071E-02 2.125973 at 20iterations 1.2642380E-03 0.2053790 at 30iterations 1.2350432E-04 1.7904282E-02 at 40iterations 1.2449167E-05 1.8539429E-03 at 50iterations finished qdiffx linear iterations at : 14:00:25 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.2449167E-05 1.8539429E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 14:00:26 3.196u 0.146s 0:04.75 70.1% 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 Mon Oct 10 2011 at 14:00:26 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 = 1966 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: 1.926894 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 1.926894 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.44824 97.70219 90.55685 assigned negative charge : -282.5023 centred at (gu) : 90.71085 98.00281 90.37973 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17553 grid for indexing accessible points = 1.400000 m= 22908 mr = 40934 m= 3744 mr = 17685 m= 205 mr = 2474 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1167 time to turn everything in is 0.4500000 number of dielectric boundary points 25442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14449 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) : 0.6422979 object centre at (A) : 15.61450 22.51700 3.412001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0542535E-02 1.3153566E-02 midg,1,midg; midg,igrid,midg 3.4293354E-02 2.5105083E-03 1,midg,midg; igrid,midg,midg 7.1220989E-03 6.5747695E-03 gauss-seidel spectral radius is 0.9985909 estimated iterations to convergence 211 setup time was (sec) 0.7100000 now iterating at: 14:00:27 rms-change max change #iterations 3.614187 187.1797 at 10iterations 1.671118 60.40022 at 20iterations 0.7751390 28.35138 at 30iterations 0.3585857 12.51795 at 40iterations 0.1657362 6.116226 at 50iterations 7.6524407E-02 2.662762 at 60iterations 3.5347216E-02 1.327377 at 70iterations 1.6388098E-02 0.5590351 at 80iterations 7.5753452E-03 0.2731619 at 90iterations 3.5011843E-03 0.1340928 at 100iterations 1.6204356E-03 5.1988602E-02 at 110iterations 7.5238821E-04 2.8544426E-02 at 120iterations finished qdiffx linear iterations at : 14:00:34 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 7.5238821E-04 2.8544426E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 14:00:34 7.226u 0.218s 0:07.97 93.2% 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 14:00:35 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 = 1966 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: 2.890340 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 2.890340 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.67242 101.5532 90.83527 assigned negative charge : -282.5023 centred at (gu) : 91.06643 102.0042 90.56960 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 138044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17553 grid for indexing accessible points = 1.400000 m= 72160 mr = 99061 m= 28398 mr = 60161 m= 6816 mr = 23813 m= 991 mr = 5266 m= 64 mr = 692 m= 0 mr = 40 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 1.070000 number of dielectric boundary points 57440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 14670 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) : 1.926894 object centre at (A) : 15.61450 22.51700 3.412001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9319414 2.6756996E-02 midg,1,midg; midg,igrid,midg 0.3722394 -5.3413820E-02 1,midg,midg; igrid,midg,midg 3.7937373E-02 0.1234194 gauss-seidel spectral radius is 0.9992333 estimated iterations to convergence 285 setup time was (sec) 1.350000 now iterating at: 14:00:36 rms-change max change #iterations 8.528703 466.8985 at 10iterations 4.898590 127.6176 at 20iterations 2.788431 60.09129 at 30iterations 1.588592 31.06865 at 40iterations 0.9045552 20.05239 at 50iterations 0.5150038 11.31235 at 60iterations 0.2923809 5.921529 at 70iterations 0.1661051 3.249489 at 80iterations 9.4274208E-02 1.909719 at 90iterations 5.3493224E-02 1.125081 at 100iterations 3.0337375E-02 0.5809345 at 110iterations 1.7238889E-02 0.3357956 at 120iterations 9.7838445E-03 0.1944771 at 130iterations 5.5599674E-03 0.1045657 at 140iterations 3.1558729E-03 6.0935020E-02 at 150iterations 1.7922509E-03 3.8152695E-02 at 160iterations 1.0188812E-03 2.2493362E-02 at 170iterations 5.7765801E-04 1.0961533E-02 at 180iterations finished qdiffx linear iterations at : 14:00:46 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 5.7765801E-04 1.0961533E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 14:00:47 11.358u 0.172s 0:12.01 95.9% 0+0k 0+0io 0pf+0w