Mon Oct 10 17:17:16 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+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 17:17:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5422530 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 0.5422530 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 409.2815 centred at (gu) : 91.29331 90.66173 91.35301 assigned negative charge : -397.2824 centred at (gu) : 91.27976 90.74292 91.20087 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5272 nv = 96 ne = 84 npr = 52915 no. pairs analyzed = 52915 no. exposed pairs = 4051 no. arc points = 28522 no. surface atoms = 1331 nbur = 1421 mkacc time = 0.1300000 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 = 1.568000 m= 220 mr = 2315 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2828 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0938363E-10 1.9639272E-09 midg,1,midg; midg,igrid,midg 8.8961705E-10 2.4440375E-10 1,midg,midg; igrid,midg,midg 4.1406661E-10 9.6419750E-10 gauss-seidel spectral radius is 0.9824612 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 17:17:17 rms-change max change #iterations 6.7475937E-02 14.75551 at 10iterations 4.2243418E-03 0.8373375 at 20iterations 2.7763285E-04 4.8580170E-02 at 30iterations 1.9293664E-05 3.5934448E-03 at 40iterations 1.6120879E-06 3.3378601E-04 at 50iterations finished qdiffx linear iterations at : 17:17:20 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.6120879E-06 3.3378601E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 17:17:20 3.637u 0.229s 0:04.32 89.1% 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 17:17:20 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.626759 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 1.626759 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 409.2815 centred at (gu) : 93.87905 91.98419 94.05845 assigned negative charge : -397.2824 centred at (gu) : 93.83894 92.22834 93.60226 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 57470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28522 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16838 mr = 35457 m= 1816 mr = 10528 m= 55 mr = 779 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 0.4600000 number of dielectric boundary points 29414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19984 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) : 0.5422530 object centre at (A) : 0.1199999 1.552000 55.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9384202E-02 1.8693333E-02 midg,1,midg; midg,igrid,midg 1.7511422E-02 9.9399127E-03 1,midg,midg; igrid,midg,midg -1.2930166E-03 2.7795422E-03 gauss-seidel spectral radius is 0.9981541 estimated iterations to convergence 185 setup time was (sec) 0.7800000 now iterating at: 17:17:21 rms-change max change #iterations 3.094659 168.2262 at 10iterations 1.265433 54.55886 at 20iterations 0.5215474 20.75100 at 30iterations 0.2137588 9.627960 at 40iterations 8.8290147E-02 3.535210 at 50iterations 3.6450002E-02 1.393092 at 60iterations 1.5076685E-02 0.6047516 at 70iterations 6.1854613E-03 0.2294298 at 80iterations 2.5659644E-03 9.2739105E-02 at 90iterations 1.0575773E-03 4.2968750E-02 at 100iterations 4.3681025E-04 1.6897202E-02 at 110iterations 1.8076970E-04 6.4373016E-03 at 120iterations finished qdiffx linear iterations at : 17:17:28 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.8076970E-04 6.4373016E-03 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 17:17:29 8.137u 0.254s 0:08.88 94.3% 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 17:17:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.440139 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 2.440139 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 409.2815 centred at (gu) : 95.81839 92.97619 96.08752 assigned negative charge : -397.2824 centred at (gu) : 95.75834 93.34256 95.40334 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 133397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28522 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 57674 mr = 88024 m= 16225 mr = 42898 m= 2850 mr = 11302 m= 255 mr = 1711 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 2146 time to turn everything in is 1.150000 number of dielectric boundary points 66377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20900 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) : 1.626759 object centre at (A) : 0.1199999 1.552000 55.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3897738 0.3375766 midg,1,midg; midg,igrid,midg 0.2353808 7.8135014E-02 1,midg,midg; igrid,midg,midg 6.4261355E-03 3.5869502E-02 gauss-seidel spectral radius is 0.9991281 estimated iterations to convergence 268 setup time was (sec) 1.470000 now iterating at: 17:17:31 rms-change max change #iterations 8.206569 287.0732 at 10iterations 4.640897 165.9150 at 20iterations 2.604102 67.44739 at 30iterations 1.451667 37.36274 at 40iterations 0.8042758 19.27449 at 50iterations 0.4449013 10.22953 at 60iterations 0.2454400 5.508293 at 70iterations 0.1346584 3.455329 at 80iterations 7.4289456E-02 1.730938 at 90iterations 4.0670693E-02 0.9191470 at 100iterations 2.2336561E-02 0.5221061 at 110iterations 1.2238612E-02 0.2779484 at 120iterations 6.7144455E-03 0.1479006 at 130iterations 3.6743325E-03 9.1881752E-02 at 140iterations 2.0129823E-03 4.3304205E-02 at 150iterations 1.1048528E-03 2.5711060E-02 at 160iterations 6.0436840E-04 1.3298035E-02 at 170iterations 3.3090441E-04 8.5611343E-03 at 180iterations finished qdiffx linear iterations at : 17:17:42 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 3.3090441E-04 8.5611343E-03 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 17:17:43 13.119u 0.286s 0:14.11 94.8% 0+0k 0+0io 0pf+0w