Tue Oct 11 06:30:42 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 06:30:42 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 = 2010 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: 0.7052298 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 0.7052298 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 90.40401 90.62485 89.49856 assigned negative charge : -302.7272 centred at (gu) : 90.22408 90.60377 89.46856 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6805 nv = 96 ne = 84 npr = 39744 no. pairs analyzed = 39744 no. exposed pairs = 2460 no. arc points = 16934 no. surface atoms = 840 nbur = 1170 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 479 mr = 3930 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1660 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0483745E-08 6.6723963E-08 midg,1,midg; midg,igrid,midg 4.4615518E-08 7.8122405E-08 1,midg,midg; igrid,midg,midg -2.1779867E-08 1.5197296E-07 gauss-seidel spectral radius is 0.9895137 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 06:30:43 rms-change max change #iterations 0.1937523 28.89490 at 10iterations 2.3464130E-02 3.666796 at 20iterations 2.9583215E-03 0.3697648 at 30iterations 4.1903899E-04 6.7863464E-02 at 40iterations 7.4593176E-05 1.1367798E-02 at 50iterations finished qdiffx linear iterations at : 06:30:47 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 7.4593176E-05 1.1367798E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 06:30:47 4.404u 0.413s 0:05.32 90.4% 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 Tue Oct 11 2011 at 06:30:47 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 = 2010 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: 2.115690 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 2.115690 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 91.21177 91.87491 88.49541 assigned negative charge : -302.7272 centred at (gu) : 90.67230 91.81142 88.40583 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 72440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 29024 mr = 51384 m= 5655 mr = 22048 m= 558 mr = 3744 m= 10 mr = 278 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 30233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15257 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) : 0.7052298 object centre at (A) : 1.512000 -8.817999 11.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9041573E-02 4.6799287E-02 midg,1,midg; midg,igrid,midg 2.9928191E-03 3.5101201E-02 1,midg,midg; igrid,midg,midg 1.6600365E-02 4.5972001E-02 gauss-seidel spectral radius is 0.9988197 estimated iterations to convergence 230 setup time was (sec) 0.9100000 now iterating at: 06:30:49 rms-change max change #iterations 4.481348 166.6292 at 10iterations 2.213604 81.99763 at 20iterations 1.093827 39.17742 at 30iterations 0.5398157 16.51340 at 40iterations 0.2673542 7.998299 at 50iterations 0.1325681 4.068474 at 60iterations 6.5365441E-02 2.223750 at 70iterations 3.2620098E-02 0.9718933 at 80iterations 1.6108785E-02 0.5216217 at 90iterations 8.0094775E-03 0.2490934 at 100iterations 3.9860238E-03 0.1183715 at 110iterations 1.9932785E-03 6.1738968E-02 at 120iterations finished qdiffx linear iterations at : 06:30:58 total time elapsed so far: 10.35000 # loops : 120 mean,max change (kT/e) : 1.9932785E-03 6.1738968E-02 energy calculations done at 10.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.52000 DelPhi exited at 06:30:59 10.520u 0.437s 0:11.50 95.2% 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 06:30:59 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 = 2010 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: 3.173534 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): -20.68800 23.71200 ymin,ymax (A): -28.67600 11.04000 zmin,zma (A): -13.75200 36.72800 x,y,z range (A): 44.40000 39.71600 50.48000 scale (grids/A): 3.173534 object centre (A): 1.512000 -8.817999 11.48800 number of atom coordinates read : 2010 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 91.81768 92.81236 87.74323 assigned negative charge : -302.7272 centred at (gu) : 91.00859 92.71719 87.60880 start vw surface at 0.1100000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 167069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 90384 mr = 123692 m= 36794 mr = 75211 m= 10570 mr = 30224 m= 2128 mr = 8187 m= 234 mr = 1546 m= 6 mr = 147 m= 0 mr = 2 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 68176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15368 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) : 2.115690 object centre at (A) : 1.512000 -8.817999 11.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7227380 0.3664465 midg,1,midg; midg,igrid,midg -7.1375337E-03 0.2821892 1,midg,midg; igrid,midg,midg 0.2642502 0.3681082 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.200000 now iterating at: 06:31:01 rms-change max change #iterations 10.02950 441.0824 at 10iterations 5.916722 118.7728 at 20iterations 3.491576 80.76676 at 30iterations 2.054145 44.87353 at 40iterations 1.205657 21.83274 at 50iterations 0.7083760 14.13536 at 60iterations 0.4148906 7.488750 at 70iterations 0.2429842 4.426010 at 80iterations 0.1420224 2.581223 at 90iterations 8.3005764E-02 1.687937 at 100iterations 4.8743166E-02 0.8414612 at 110iterations 2.8636677E-02 0.5315399 at 120iterations 1.6901612E-02 0.3216605 at 130iterations 1.0092031E-02 0.2052116 at 140iterations 6.1295917E-03 0.1199875 at 150iterations 3.8395817E-03 7.4398041E-02 at 160iterations 2.5269436E-03 4.8027039E-02 at 170iterations 1.7494116E-03 3.3477783E-02 at 180iterations finished qdiffx linear iterations at : 06:31:17 total time elapsed so far: 17.81000 # loops : 180 mean,max change (kT/e) : 1.7494116E-03 3.3477783E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 06:31:18 17.991u 0.460s 0:18.99 97.1% 0+0k 0+0io 0pf+0w