Sat Oct 8 16:00:35 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 8 2011 at 16:00:35 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 = 2327 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: 0.6475671 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 0.6475671 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.43456 88.75291 90.32220 assigned negative charge : -338.3788 centred at (gu) : 90.47182 88.87332 90.36617 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 47826 no. pairs analyzed = 47826 no. exposed pairs = 2797 no. arc points = 19701 no. surface atoms = 961 nbur = 1366 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3676 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1937 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1687572E-08 1.6318236E-09 midg,1,midg; midg,igrid,midg 2.8527136E-08 -6.1478524E-09 1,midg,midg; igrid,midg,midg 1.0662345E-08 2.5881264E-09 gauss-seidel spectral radius is 0.9876181 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 16:00:36 rms-change max change #iterations 0.1447658 27.62270 at 10iterations 1.4492369E-02 2.239691 at 20iterations 1.4990716E-03 0.2313633 at 30iterations 1.6362259E-04 2.4726868E-02 at 40iterations 2.2096245E-05 3.2036304E-03 at 50iterations finished qdiffx linear iterations at : 16:00:40 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 2.2096245E-05 3.2036304E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 16:00:40 4.425u 0.406s 0:05.10 94.5% 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 8 2011 at 16:00:40 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 = 2327 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: 1.942701 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 1.942701 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.30347 86.25819 90.96588 assigned negative charge : -338.3788 centred at (gu) : 91.41531 86.61982 91.09844 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 25146 mr = 49438 m= 4337 mr = 18762 m= 282 mr = 2875 m= 2 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.5700000 number of dielectric boundary points 29156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17574 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) : 0.6475671 object centre at (A) : 22.02200 6.594000 8.886498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5803961E-02 -1.4573185E-02 midg,1,midg; midg,igrid,midg 2.8165482E-02 -4.7901603E-03 1,midg,midg; igrid,midg,midg 8.4228683E-03 -3.2613616E-02 gauss-seidel spectral radius is 0.9986567 estimated iterations to convergence 216 setup time was (sec) 0.8700000 now iterating at: 16:00:42 rms-change max change #iterations 4.109083 216.2380 at 10iterations 1.931278 74.30812 at 20iterations 0.9095766 28.67873 at 30iterations 0.4286246 15.45371 at 40iterations 0.2022461 6.828400 at 50iterations 9.5529169E-02 3.225483 at 60iterations 4.4917159E-02 1.414159 at 70iterations 2.1200269E-02 0.7100115 at 80iterations 1.0003903E-02 0.3175249 at 90iterations 4.7211605E-03 0.1461830 at 100iterations 2.2298163E-03 7.0508957E-02 at 110iterations 1.0537271E-03 3.2635689E-02 at 120iterations finished qdiffx linear iterations at : 16:00:51 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.0537271E-03 3.2635689E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 16:00:52 10.567u 0.451s 0:11.29 97.5% 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 8 2011 at 16:00:52 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 = 2327 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: 2.914052 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 2.914052 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.95503 84.38723 91.44881 assigned negative charge : -338.3788 centred at (gu) : 92.12289 84.92968 91.64764 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 163774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 81177 mr = 120049 m= 29906 mr = 66802 m= 7926 mr = 24359 m= 1258 mr = 6260 m= 72 mr = 885 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 3432 time to turn everything in is 1.510000 number of dielectric boundary points 65722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 17838 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) : 1.942701 object centre at (A) : 22.02200 6.594000 8.886498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1655290 -0.1876848 midg,1,midg; midg,igrid,midg 0.2168090 -6.5886743E-02 1,midg,midg; igrid,midg,midg 8.3724625E-02 -0.4739901 gauss-seidel spectral radius is 0.9992566 estimated iterations to convergence 289 setup time was (sec) 1.840000 now iterating at: 16:00:54 rms-change max change #iterations 9.453959 515.1047 at 10iterations 5.509984 119.3760 at 20iterations 3.187998 70.99432 at 30iterations 1.849780 36.75147 at 40iterations 1.069025 21.15852 at 50iterations 0.6161739 12.09066 at 60iterations 0.3542834 6.461035 at 70iterations 0.2043023 4.097973 at 80iterations 0.1176255 2.256486 at 90iterations 6.7624316E-02 1.213261 at 100iterations 3.8957663E-02 0.7946777 at 110iterations 2.2336615E-02 0.4557931 at 120iterations 1.2829542E-02 0.2553759 at 130iterations 7.3771328E-03 0.1379318 at 140iterations 4.2458577E-03 7.4685693E-02 at 150iterations 2.4311314E-03 4.5217305E-02 at 160iterations 1.3979523E-03 2.6041031E-02 at 170iterations 8.0318830E-04 1.5056610E-02 at 180iterations finished qdiffx linear iterations at : 16:01:10 total time elapsed so far: 17.65000 # loops : 180 mean,max change (kT/e) : 8.0318830E-04 1.5056610E-02 energy calculations done at 17.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.81000 DelPhi exited at 16:01:10 17.815u 0.494s 0:18.60 98.3% 0+0k 0+0io 0pf+0w