Wed Dec 28 11:02:00 PST 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 Wed Dec 28 2011 at 11:02:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6528756 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 0.6528756 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.28774 92.59876 90.10880 assigned negative charge : -285.8263 centred at (gu) : 90.42319 92.75513 90.03673 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 40890 no. pairs analyzed = 40890 no. exposed pairs = 2481 no. arc points = 17403 no. surface atoms = 832 nbur = 1132 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3107 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1714 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8509098E-09 1.3677285E-08 midg,1,midg; midg,igrid,midg 1.3513561E-08 -2.5490021E-08 1,midg,midg; igrid,midg,midg 1.9584094E-08 -1.2495570E-08 gauss-seidel spectral radius is 0.9877849 estimated iterations to convergence 74 setup time was (sec) 0.6500000 now iterating at: 11:02:01 rms-change max change #iterations 0.1334661 22.23452 at 10iterations 1.3921703E-02 2.064108 at 20iterations 1.4220463E-03 0.2024002 at 30iterations 1.4579615E-04 2.6260376E-02 at 40iterations 1.5181871E-05 2.4318695E-03 at 50iterations finished qdiffx linear iterations at : 11:02:07 total time elapsed so far: 6.220000 # loops : 50 mean,max change (kT/e) : 1.5181871E-05 2.4318695E-03 energy calculations done at 6.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.400000 DelPhi exited at 11:02:10 6.408u 0.802s 0:09.47 76.0% 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 Wed Dec 28 2011 at 11:02:10 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.958627 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 1.958627 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.86301 97.79621 90.32655 assigned negative charge : -285.8263 centred at (gu) : 91.26990 98.26557 90.11040 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17403 grid for indexing accessible points = 1.400000 m= 21986 mr = 41578 m= 3801 mr = 16606 m= 251 mr = 2541 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.6300000 number of dielectric boundary points 25755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14476 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) : 0.6528756 object centre at (A) : 15.11100 22.25750 3.496000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6954732E-02 1.7140081E-02 midg,1,midg; midg,igrid,midg 4.6503738E-02 -1.2290425E-02 1,midg,midg; igrid,midg,midg 5.9768539E-03 -9.9176671E-03 gauss-seidel spectral radius is 0.9986289 estimated iterations to convergence 214 setup time was (sec) 1.180000 now iterating at: 11:02:12 rms-change max change #iterations 3.780005 157.1967 at 10iterations 1.764243 65.67427 at 20iterations 0.8266250 29.75372 at 30iterations 0.3859946 13.26429 at 40iterations 0.1803974 6.813293 at 50iterations 8.4165432E-02 2.975034 at 60iterations 3.9348409E-02 1.534313 at 70iterations 1.8363262E-02 0.6676750 at 80iterations 8.6056655E-03 0.3084822 at 90iterations 4.0100836E-03 0.1742570 at 100iterations 1.8706867E-03 6.3552856E-02 at 110iterations 8.7688898E-04 2.9582977E-02 at 120iterations finished qdiffx linear iterations at : 11:02:29 total time elapsed so far: 18.53000 # loops : 120 mean,max change (kT/e) : 8.7688898E-04 2.9582977E-02 energy calculations done at 18.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.71000 DelPhi exited at 11:02:31 18.718u 0.833s 0:20.90 93.4% 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 Wed Dec 28 2011 at 11:02:31 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.937940 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): -4.459000 34.68100 ymin,ymax (A): -3.417000 47.93200 zmin,zma (A): -23.76800 30.76000 x,y,z range (A): 39.14000 51.34900 54.52800 scale (grids/A): 2.937940 object centre (A): 15.11100 22.25750 3.496000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.29472 101.6943 90.48993 assigned negative charge : -285.8263 centred at (gu) : 91.90497 102.3984 90.16554 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 139783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17403 grid for indexing accessible points = 1.400000 m= 70476 mr = 100524 m= 26470 mr = 58184 m= 7003 mr = 21856 m= 1135 mr = 5546 m= 68 mr = 769 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3091 time to turn everything in is 1.590000 number of dielectric boundary points 58037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 14656 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) : 1.958627 object centre at (A) : 15.11100 22.25750 3.496000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.099015 4.1065622E-02 midg,1,midg; midg,igrid,midg 0.5002632 -0.1829390 1,midg,midg; igrid,midg,midg 2.3583841E-02 -6.0111027E-02 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.190000 now iterating at: 11:02:34 rms-change max change #iterations 8.726357 409.4377 at 10iterations 4.997549 112.4288 at 20iterations 2.850805 62.65718 at 30iterations 1.627830 33.14043 at 40iterations 0.9288672 18.12134 at 50iterations 0.5284193 10.63196 at 60iterations 0.3013585 6.915812 at 70iterations 0.1717032 3.285868 at 80iterations 9.7911835E-02 2.041534 at 90iterations 5.5712976E-02 1.139123 at 100iterations 3.1736124E-02 0.6771610 at 110iterations 1.8131733E-02 0.3602295 at 120iterations 1.0304192E-02 0.2057147 at 130iterations 5.8707804E-03 0.1143446 at 140iterations 3.3439174E-03 6.0495377E-02 at 150iterations 1.9045698E-03 3.8438082E-02 at 160iterations 1.0876781E-03 2.1851540E-02 at 170iterations 6.1884033E-04 1.1724472E-02 at 180iterations finished qdiffx linear iterations at : 11:03:03 total time elapsed so far: 30.36000 # loops : 180 mean,max change (kT/e) : 6.1884033E-04 1.1724472E-02 energy calculations done at 30.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.54000 DelPhi exited at 11:03:03 30.547u 0.907s 0:32.08 98.0% 0+0k 0+0io 0pf+0w