Sun Oct 9 08:03:50 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 Sun Oct 9 2011 at 08:03:50 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6948375 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 0.6948375 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 341.1554 centred at (gu) : 90.04195 91.01601 90.22741 assigned negative charge : -344.6557 centred at (gu) : 90.07397 91.09017 90.32966 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7504 nv = 96 ne = 84 npr = 44249 no. pairs analyzed = 44249 no. exposed pairs = 2898 no. arc points = 20809 no. surface atoms = 966 nbur = 1266 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4093 m= 6 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1700000 number of dielectric boundary points 3855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1985 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8299 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9223728E-08 -6.6593458E-08 midg,1,midg; midg,igrid,midg 7.0218444E-09 -6.3574937E-08 1,midg,midg; igrid,midg,midg -8.1550011E-09 -3.4741817E-08 gauss-seidel spectral radius is 0.9892328 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 08:03:51 rms-change max change #iterations 0.2011721 31.89527 at 10iterations 2.3622923E-02 3.413765 at 20iterations 2.8096547E-03 0.4007416 at 30iterations 3.3148171E-04 4.7065735E-02 at 40iterations 3.9290066E-05 5.0428212E-03 at 50iterations finished qdiffx linear iterations at : 08:03:54 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 3.9290066E-05 5.0428212E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:03:54 3.465u 0.183s 0:03.91 93.0% 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 Sun Oct 9 2011 at 08:03:54 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.084512 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 2.084512 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 341.1554 centred at (gu) : 90.12544 93.04765 90.68169 assigned negative charge : -344.6557 centred at (gu) : 90.22163 93.27042 90.98900 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20809 grid for indexing accessible points = 1.400000 m= 32003 mr = 54246 m= 6631 mr = 24081 m= 663 mr = 4471 m= 25 mr = 324 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 485 time to turn everything in is 0.3900000 number of dielectric boundary points 35305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16582 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) : 0.6948375 object centre at (A) : 27.34350 0.8055000 5.348500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3274234E-03 -4.0542133E-02 midg,1,midg; midg,igrid,midg 2.2224335E-02 -1.1669296E-03 1,midg,midg; igrid,midg,midg -1.2207201E-03 -3.4524258E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 0.6100000 now iterating at: 08:03:55 rms-change max change #iterations 4.821404 211.6240 at 10iterations 2.376597 82.68896 at 20iterations 1.180555 39.41396 at 30iterations 0.5791909 18.53965 at 40iterations 0.2868099 8.912427 at 50iterations 0.1414699 4.544711 at 60iterations 7.0116788E-02 2.248852 at 70iterations 3.4499675E-02 1.009972 at 80iterations 1.7095152E-02 0.5350990 at 90iterations 8.4537510E-03 0.2524109 at 100iterations 4.1797813E-03 0.1248093 at 110iterations 2.0645184E-03 5.8416843E-02 at 120iterations finished qdiffx linear iterations at : 08:04:02 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 2.0645184E-03 5.8416843E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 08:04:03 8.062u 0.229s 0:08.62 96.0% 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 Sun Oct 9 2011 at 08:04:03 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.126769 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 3.126769 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 341.1554 centred at (gu) : 90.18829 94.57133 91.02254 assigned negative charge : -344.6557 centred at (gu) : 90.33242 94.90562 91.48348 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 181980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20809 grid for indexing accessible points = 1.400000 m= 98043 mr = 130631 m= 41709 mr = 80823 m= 12578 mr = 34356 m= 2631 mr = 9760 m= 310 mr = 1891 m= 14 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1584 time to turn everything in is 1.230000 number of dielectric boundary points 79643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 16720 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) : 2.084512 object centre at (A) : 27.34350 0.8055000 5.348500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4257941E-02 -0.2686187 midg,1,midg; midg,igrid,midg 0.7970055 9.0622954E-02 1,midg,midg; igrid,midg,midg -3.2248668E-02 -0.3094470 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.490000 now iterating at: 08:04:04 rms-change max change #iterations 10.84024 500.7235 at 10iterations 6.372133 127.8145 at 20iterations 3.735914 80.26221 at 30iterations 2.192379 39.92816 at 40iterations 1.283783 23.07652 at 50iterations 0.7515147 13.11844 at 60iterations 0.4400291 8.196840 at 70iterations 0.2572169 4.613390 at 80iterations 0.1499980 2.597767 at 90iterations 8.7585688E-02 1.456755 at 100iterations 5.1277734E-02 0.8509769 at 110iterations 2.9860491E-02 0.4911499 at 120iterations 1.7410278E-02 0.2843599 at 130iterations 1.0166711E-02 0.1731148 at 140iterations 5.9454418E-03 0.1010704 at 150iterations 3.4673372E-03 5.9020996E-02 at 160iterations 2.0338760E-03 3.7330627E-02 at 170iterations 1.1952524E-03 1.9220352E-02 at 180iterations finished qdiffx linear iterations at : 08:04:17 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 1.1952524E-03 1.9220352E-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 08:04:17 14.100u 0.264s 0:14.65 98.0% 0+0k 0+0io 0pf+0w