Tue Oct 11 06:24:45 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 Tue Oct 11 2011 at 06:24:45 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 = 2135 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: 0.6591493 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 0.6591493 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 88.95655 90.56250 90.24517 assigned negative charge : -320.1811 centred at (gu) : 88.96046 90.64340 90.14817 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6134 nv = 96 ne = 84 npr = 43189 no. pairs analyzed = 43189 no. exposed pairs = 2536 no. arc points = 17622 no. surface atoms = 874 nbur = 1261 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3434 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7258 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5642652E-10 3.3128245E-08 midg,1,midg; midg,igrid,midg 2.5810481E-08 3.4358114E-09 1,midg,midg; igrid,midg,midg 2.0750113E-08 1.2632953E-08 gauss-seidel spectral radius is 0.9880213 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 06:24:46 rms-change max change #iterations 0.1488796 28.13069 at 10iterations 1.6032539E-02 2.366868 at 20iterations 1.8117419E-03 0.2627621 at 30iterations 2.7123114E-04 3.4873962E-02 at 40iterations 6.1511440E-05 8.8081360E-03 at 50iterations finished qdiffx linear iterations at : 06:24:49 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.1511440E-05 8.8081360E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:24:49 3.402u 0.175s 0:03.88 92.0% 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 Tue Oct 11 2011 at 06:24:49 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 = 2135 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: 1.977448 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 1.977448 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 86.86963 91.68747 90.73570 assigned negative charge : -320.1811 centred at (gu) : 86.88148 91.93024 90.44443 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 23916 mr = 46193 m= 3669 mr = 17738 m= 233 mr = 2254 m= 3 mr = 101 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 0.3200000 number of dielectric boundary points 27139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 15804 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) : 0.6591493 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0769142E-02 2.3000462E-02 midg,1,midg; midg,igrid,midg 2.2868982E-02 7.2678505E-03 1,midg,midg; igrid,midg,midg 7.0204467E-02 1.1326925E-02 gauss-seidel spectral radius is 0.9986746 estimated iterations to convergence 218 setup time was (sec) 0.5200000 now iterating at: 06:24:50 rms-change max change #iterations 4.120327 225.2797 at 10iterations 1.955155 73.39421 at 20iterations 0.9282928 33.76254 at 30iterations 0.4390184 16.15998 at 40iterations 0.2074977 7.090267 at 50iterations 9.8678380E-02 3.218517 at 60iterations 4.6813898E-02 1.651609 at 70iterations 2.2159174E-02 0.7551079 at 80iterations 1.0562886E-02 0.3451636 at 90iterations 5.0422684E-03 0.1951971 at 100iterations 2.4226201E-03 7.6654434E-02 at 110iterations 1.1715095E-03 3.7015811E-02 at 120iterations finished qdiffx linear iterations at : 06:24:57 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.1715095E-03 3.7015811E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 06:24:58 7.761u 0.224s 0:08.26 96.6% 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 Tue Oct 11 2011 at 06:24:58 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 = 2135 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: 2.966172 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 2.966172 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 85.30428 92.53111 91.10352 assigned negative charge : -320.1811 centred at (gu) : 85.32214 92.89539 90.66659 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 151570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 77446 mr = 111630 m= 27758 mr = 63697 m= 6626 mr = 22391 m= 991 mr = 4900 m= 72 mr = 724 m= 0 mr = 33 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 61088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 16056 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) : 1.977448 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2063599 0.2443832 midg,1,midg; midg,igrid,midg 0.2315488 6.8991594E-02 1,midg,midg; igrid,midg,midg 1.006895 -0.2431881 gauss-seidel spectral radius is 0.9992560 estimated iterations to convergence 289 setup time was (sec) 1.080000 now iterating at: 06:24:59 rms-change max change #iterations 9.441564 381.8578 at 10iterations 5.512925 132.9038 at 20iterations 3.210115 69.70776 at 30iterations 1.868238 37.46991 at 40iterations 1.086019 22.76314 at 50iterations 0.6272663 12.22760 at 60iterations 0.3640132 8.069982 at 70iterations 0.2100434 4.569138 at 80iterations 0.1212175 2.233643 at 90iterations 6.9829501E-02 1.317976 at 100iterations 4.0371496E-02 0.7282448 at 110iterations 2.3392299E-02 0.4693050 at 120iterations 1.3563226E-02 0.2886114 at 130iterations 7.9319226E-03 0.1571178 at 140iterations 4.7001638E-03 9.3309402E-02 at 150iterations 2.8465874E-03 6.0981750E-02 at 160iterations 1.7881399E-03 3.5526276E-02 at 170iterations 1.1776000E-03 2.1335602E-02 at 180iterations finished qdiffx linear iterations at : 06:25:10 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 1.1776000E-03 2.1335602E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 06:25:10 12.278u 0.229s 0:12.81 97.5% 0+0k 0+0io 0pf+0w