Mon Oct 10 10:09:00 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 10:09:00 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5815948 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 0.5815948 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.014015 assigned positive charge : 395.9691 centred at (gu) : 88.49195 88.22539 87.44348 assigned negative charge : -389.9554 centred at (gu) : 88.54895 88.05383 87.37556 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 52504 no. pairs analyzed = 52504 no. exposed pairs = 4168 no. arc points = 30358 no. surface atoms = 1388 nbur = 1333 mkacc time = 0.1400000 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 = 1.512000 m= 294 mr = 2651 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2919 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8031672E-11 1.5678503E-09 midg,1,midg; midg,igrid,midg -3.1818266E-09 3.2011602E-09 1,midg,midg; igrid,midg,midg 3.6919727E-09 2.3554433E-10 gauss-seidel spectral radius is 0.9847388 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 10:09:01 rms-change max change #iterations 9.2089228E-02 13.79608 at 10iterations 7.2591496E-03 1.249344 at 20iterations 5.6769809E-04 0.1172600 at 30iterations 4.9987448E-05 8.6669922E-03 at 40iterations 6.2460572E-06 1.2016296E-03 at 50iterations finished qdiffx linear iterations at : 10:09:05 total time elapsed so far: 4.570000 # loops : 50 mean,max change (kT/e) : 6.2460572E-06 1.2016296E-03 energy calculations done at 4.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 10:09:06 4.745u 0.438s 0:05.44 95.0% 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 Mon Oct 10 2011 at 10:09:06 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.744784 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 1.744784 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.014015 assigned positive charge : 395.9691 centred at (gu) : 85.47547 84.67588 82.33028 assigned negative charge : -389.9554 centred at (gu) : 85.64680 84.16131 82.12657 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30358 grid for indexing accessible points = 1.400000 m= 20869 mr = 39722 m= 2697 mr = 13165 m= 91 mr = 1333 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 35571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19990 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) : 0.5815948 object centre at (A) : 7.773499 -30.20050 29.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6362634E-02 3.5939359E-03 midg,1,midg; midg,igrid,midg 1.8236373E-02 3.2913737E-02 1,midg,midg; igrid,midg,midg 1.1959651E-02 5.0898995E-03 gauss-seidel spectral radius is 0.9984125 estimated iterations to convergence 199 setup time was (sec) 0.8800000 now iterating at: 10:09:26 rms-change max change #iterations 3.600736 174.6427 at 10iterations 1.586029 60.02390 at 20iterations 0.6964892 24.08879 at 30iterations 0.3058500 11.08917 at 40iterations 0.1358417 4.805870 at 50iterations 5.9533883E-02 2.551559 at 60iterations 2.6313731E-02 0.8838034 at 70iterations 1.1577289E-02 0.3954735 at 80iterations 5.0897733E-03 0.1850643 at 90iterations 2.2531613E-03 7.9738617E-02 at 100iterations 9.9247613E-04 4.0912628E-02 at 110iterations 4.3767097E-04 1.6654730E-02 at 120iterations finished qdiffx linear iterations at : 10:09:36 total time elapsed so far: 10.91000 # loops : 120 mean,max change (kT/e) : 4.3767097E-04 1.6654730E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 10:09:36 11.074u 0.571s 0:30.73 37.8% 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 10:09:37 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.617177 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): -18.12300 33.67000 ymin,ymax (A): -59.33300 -1.068000 zmin,zma (A): -1.137000 60.07400 x,y,z range (A): 51.79300 58.26500 61.21100 scale (grids/A): 2.617177 object centre (A): 7.773499 -30.20050 29.46850 number of atom coordinates read : 2721 total number of charged atoms : 2572 net assigned charge : 6.014015 assigned positive charge : 395.9691 centred at (gu) : 83.21313 82.01374 78.49529 assigned negative charge : -389.9554 centred at (gu) : 83.47008 81.24194 78.18972 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 152911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30358 grid for indexing accessible points = 1.400000 m= 67668 mr = 98321 m= 22326 mr = 50028 m= 4437 mr = 16136 m= 363 mr = 2780 m= 9 mr = 162 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 80288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 20573 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) : 1.744784 object centre at (A) : 7.773499 -30.20050 29.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4401183 4.4232294E-02 midg,1,midg; midg,igrid,midg 0.3321067 0.4036087 1,midg,midg; igrid,midg,midg 4.6502113E-02 5.8387566E-02 gauss-seidel spectral radius is 0.9992250 estimated iterations to convergence 284 setup time was (sec) 1.800000 now iterating at: 10:09:40 rms-change max change #iterations 9.169497 310.6550 at 10iterations 5.424425 154.4389 at 20iterations 3.160567 73.41826 at 30iterations 1.827513 45.40278 at 40iterations 1.052960 26.91776 at 50iterations 0.6065815 13.88627 at 60iterations 0.3476475 7.929378 at 70iterations 0.1984963 4.401321 at 80iterations 0.1130180 3.161140 at 90iterations 6.4371862E-02 1.650558 at 100iterations 3.6633305E-02 0.7925110 at 110iterations 2.0802153E-02 0.4228487 at 120iterations 1.1833984E-02 0.2616806 at 130iterations 6.7312419E-03 0.1311703 at 140iterations 3.8071200E-03 8.2889318E-02 at 150iterations 2.1617126E-03 4.3323755E-02 at 160iterations 1.2230874E-03 2.7986050E-02 at 170iterations 6.9616782E-04 1.4796257E-02 at 180iterations finished qdiffx linear iterations at : 10:09:57 total time elapsed so far: 18.91000 # loops : 180 mean,max change (kT/e) : 6.9616782E-04 1.4796257E-02 energy calculations done at 18.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.11000 DelPhi exited at 10:09:58 19.111u 0.487s 0:21.02 93.1% 0+0k 0+0io 0pf+0w