Tue Oct 11 03:20:31 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 Tue Oct 11 2011 at 03:20:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 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: 0.7136700 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 0.7136700 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.5209 centred at (gu) : 91.10935 89.71883 90.63927 assigned negative charge : -282.5212 centred at (gu) : 91.12543 90.03098 90.79205 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 37128 no. pairs analyzed = 37128 no. exposed pairs = 2554 no. arc points = 18180 no. surface atoms = 862 nbur = 1061 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 3642 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.1600000 number of dielectric boundary points 3541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1565 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7117 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1180969E-07 -3.4890302E-08 midg,1,midg; midg,igrid,midg 2.1612938E-07 -1.0953058E-07 1,midg,midg; igrid,midg,midg 4.6724995E-08 5.0345285E-08 gauss-seidel spectral radius is 0.9897572 estimated iterations to convergence 80 setup time was (sec) 0.3300000 now iterating at: 03:20:32 rms-change max change #iterations 0.1974305 27.06634 at 10iterations 2.4953211E-02 4.097276 at 20iterations 3.0661437E-03 0.4133339 at 30iterations 3.8612806E-04 5.0712585E-02 at 40iterations 4.6937050E-05 6.6452026E-03 at 50iterations finished qdiffx linear iterations at : 03:20:35 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 4.6937050E-05 6.6452026E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:20:35 3.290u 0.164s 0:03.87 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 Tue Oct 11 2011 at 03:20:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 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: 2.141010 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 2.141010 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.5209 centred at (gu) : 93.32822 89.15635 91.91779 assigned negative charge : -282.5212 centred at (gu) : 93.37636 90.09295 92.37631 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 71156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18180 grid for indexing accessible points = 1.400000 m= 28062 mr = 47922 m= 5384 mr = 21028 m= 491 mr = 3339 m= 12 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 0.3500000 number of dielectric boundary points 32586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13942 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) : 0.7136700 object centre at (A) : 41.64050 12.09300 25.33250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2658876E-02 -1.8953782E-02 midg,1,midg; midg,igrid,midg 7.4771829E-02 -8.4889114E-02 1,midg,midg; igrid,midg,midg 1.4031888E-02 5.6076549E-02 gauss-seidel spectral radius is 0.9988396 estimated iterations to convergence 232 setup time was (sec) 0.5600000 now iterating at: 03:20:36 rms-change max change #iterations 4.498393 225.1165 at 10iterations 2.224180 82.06761 at 20iterations 1.104582 35.80367 at 30iterations 0.5492229 17.96088 at 40iterations 0.2722209 8.139404 at 50iterations 0.1347090 4.385450 at 60iterations 6.7030191E-02 2.216311 at 70iterations 3.3224199E-02 0.9944954 at 80iterations 1.6527016E-02 0.5459557 at 90iterations 8.1872819E-03 0.2555580 at 100iterations 4.0571094E-03 0.1396446 at 110iterations 2.0225602E-03 6.2511444E-02 at 120iterations finished qdiffx linear iterations at : 03:20:43 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 2.0225602E-03 6.2511444E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:20:44 7.649u 0.194s 0:08.33 93.9% 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 03:20:44 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 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: 3.211515 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 3.211515 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.5209 centred at (gu) : 94.99240 88.73452 92.87676 assigned negative charge : -282.5212 centred at (gu) : 95.06449 90.13944 93.56445 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18180 grid for indexing accessible points = 1.400000 m= 86448 mr = 115818 m= 35724 mr = 70908 m= 9995 mr = 29080 m= 1988 mr = 7360 m= 214 mr = 1386 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 5882 time to turn everything in is 1.070000 number of dielectric boundary points 73414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14047 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) : 2.141010 object centre at (A) : 41.64050 12.09300 25.33250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4270260 -0.2357795 midg,1,midg; midg,igrid,midg 0.4778193 -0.9609960 1,midg,midg; igrid,midg,midg 8.7028779E-02 0.6216650 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 1.300000 now iterating at: 03:20:45 rms-change max change #iterations 10.11769 356.5462 at 10iterations 6.031131 124.4455 at 20iterations 3.578903 70.43366 at 30iterations 2.116969 40.44653 at 40iterations 1.250592 23.14249 at 50iterations 0.7373348 13.44415 at 60iterations 0.4334532 8.641253 at 70iterations 0.2549953 5.038233 at 80iterations 0.1496851 2.768896 at 90iterations 8.7854177E-02 1.564909 at 100iterations 5.1566862E-02 0.9106903 at 110iterations 3.0265817E-02 0.5437469 at 120iterations 1.7714990E-02 0.3157387 at 130iterations 1.0399324E-02 0.1842537 at 140iterations 6.0886675E-03 0.1034241 at 150iterations 3.5723413E-03 6.1264992E-02 at 160iterations 2.0919782E-03 3.4168243E-02 at 170iterations 1.2276826E-03 2.2203445E-02 at 180iterations finished qdiffx linear iterations at : 03:20:56 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 1.2276826E-03 2.2203445E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 03:20:57 12.489u 0.219s 0:13.29 95.4% 0+0k 0+0io 0pf+0w