Sat Oct 15 13:13:16 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 Sat Oct 15 2011 at 13:13:16 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5297 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5197611 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): 3.195000 68.28201 ymin,ymax (A): -9.002000 52.31700 zmin,zma (A): -1.566000 66.92700 x,y,z range (A): 65.08701 61.31900 68.49300 scale (grids/A): 0.5197611 object centre (A): 35.73850 21.65750 32.68050 number of atom coordinates read : 5297 total number of charged atoms : 5150 net assigned charge : 5.530033 assigned positive charge : 815.5273 centred at (gu) : 88.21378 89.67718 88.71631 assigned negative charge : -810.0035 centred at (gu) : 88.11903 89.70071 88.63139 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9186 nv = 96 ne = 84 npr = 106760 no. pairs analyzed = 106760 no. exposed pairs = 6107 no. arc points = 42005 no. surface atoms = 2075 nbur = 3222 mkacc time = 0.1800000 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 = 1.652000 m= 354 mr = 5192 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4240 ## 599 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 12360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3819475E-10 3.5194223E-10 midg,1,midg; midg,igrid,midg 2.5067612E-10 2.6647172E-11 1,midg,midg; igrid,midg,midg -4.5773135E-10 3.3539302E-10 gauss-seidel spectral radius is 0.9810974 estimated iterations to convergence 60 setup time was (sec) 0.5300000 now iterating at: 13:13:17 rms-change max change #iterations 8.2953021E-02 12.36576 at 10iterations 9.9897813E-03 1.628006 at 20iterations 3.8278683E-03 0.6424828 at 30iterations 1.6674135E-03 0.2818756 at 40iterations 7.3084224E-04 0.1232529 at 50iterations finished qdiffx linear iterations at : 13:13:21 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 7.3084224E-04 0.1232529 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 13:13:22 3.543u 0.183s 0:05.71 65.1% 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 Sat Oct 15 2011 at 13:13:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5297 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.559283 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): 3.195000 68.28201 ymin,ymax (A): -9.002000 52.31700 zmin,zma (A): -1.566000 66.92700 x,y,z range (A): 65.08701 61.31900 68.49300 scale (grids/A): 1.559283 object centre (A): 35.73850 21.65750 32.68050 number of atom coordinates read : 5297 total number of charged atoms : 5150 net assigned charge : 5.530033 assigned positive charge : 815.5273 centred at (gu) : 84.63974 89.03030 86.14735 assigned negative charge : -810.0035 centred at (gu) : 84.35694 89.10226 85.89391 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 33657 mr = 75929 m= 3413 mr = 23965 m= 74 mr = 1663 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 40477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 531 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 38899 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) : 0.5197611 object centre at (A) : 35.73850 21.65750 32.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7246356E-02 2.6826071E-02 midg,1,midg; midg,igrid,midg 1.4713881E-02 6.2914179E-03 1,midg,midg; igrid,midg,midg -9.7018387E-03 6.5560322E-03 gauss-seidel spectral radius is 0.9982194 estimated iterations to convergence 188 setup time was (sec) 0.8100000 now iterating at: 13:13:23 rms-change max change #iterations 4.265921 158.7423 at 10iterations 1.794989 60.78135 at 20iterations 0.7582175 24.84156 at 30iterations 0.3206050 9.974400 at 40iterations 0.1360821 4.110836 at 50iterations 5.8844477E-02 1.775774 at 60iterations 2.6394404E-02 0.8622570 at 70iterations 1.3048748E-02 0.4085999 at 80iterations 7.4641732E-03 0.2762680 at 90iterations 4.8658964E-03 0.1590424 at 100iterations 3.4275306E-03 0.1109123 at 110iterations 2.4942334E-03 8.0505371E-02 at 120iterations finished qdiffx linear iterations at : 13:13:35 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 2.4942334E-03 8.0505371E-02 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 13:13:36 8.464u 0.260s 0:13.96 62.4% 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 Sat Oct 15 2011 at 13:13:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5297 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.338925 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): 3.195000 68.28201 ymin,ymax (A): -9.002000 52.31700 zmin,zma (A): -1.566000 66.92700 x,y,z range (A): 65.08701 61.31900 68.49300 scale (grids/A): 2.338925 object centre (A): 35.73850 21.65750 32.68050 number of atom coordinates read : 5297 total number of charged atoms : 5150 net assigned charge : 5.530033 assigned positive charge : 815.5273 centred at (gu) : 81.95943 88.54507 84.22063 assigned negative charge : -810.0035 centred at (gu) : 81.53529 88.65321 83.84087 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 244678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 118267 mr = 185744 m= 32913 mr = 95859 m= 5147 mr = 24958 m= 350 mr = 3362 m= 5 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 91276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 41087 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) : 1.559283 object centre at (A) : 35.73850 21.65750 32.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3565297 0.8085476 midg,1,midg; midg,igrid,midg 0.2233125 4.7370732E-02 1,midg,midg; igrid,midg,midg -0.3416769 8.7854378E-02 gauss-seidel spectral radius is 0.9991941 estimated iterations to convergence 278 setup time was (sec) 1.480000 now iterating at: 13:13:38 rms-change max change #iterations 11.23688 290.1891 at 10iterations 6.485219 132.0871 at 20iterations 3.705447 86.64520 at 30iterations 2.109894 39.31435 at 40iterations 1.198870 23.15636 at 50iterations 0.6801331 12.84285 at 60iterations 0.3850150 7.008171 at 70iterations 0.2175242 3.698212 at 80iterations 0.1230052 2.084164 at 90iterations 6.9895081E-02 1.182266 at 100iterations 3.9921124E-02 0.7346649 at 110iterations 2.3238530E-02 0.4321785 at 120iterations 1.3939719E-02 0.2665863 at 130iterations 8.7995054E-03 0.1763992 at 140iterations 5.9147277E-03 0.1258087 at 150iterations 4.2724605E-03 8.5632324E-02 at 160iterations 3.2598029E-03 6.7436218E-02 at 170iterations 2.5771975E-03 5.0895691E-02 at 180iterations finished qdiffx linear iterations at : 13:13:53 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 2.5771975E-03 5.0895691E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 13:13:53 13.478u 0.246s 0:17.61 77.8% 0+0k 0+0io 0pf+0w