Mon Oct 10 14:14:03 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 14:14:03 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6456879 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 0.6456879 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2456 net assigned charge : 6.488015 assigned positive charge : 392.9160 centred at (gu) : 89.86816 90.39381 91.39921 assigned negative charge : -386.4283 centred at (gu) : 89.95793 90.53218 91.51021 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7227 nv = 96 ne = 84 npr = 47135 no. pairs analyzed = 47135 no. exposed pairs = 3414 no. arc points = 24315 no. surface atoms = 1143 nbur = 1356 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3709 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2387 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9561588E-08 -5.3661231E-09 midg,1,midg; midg,igrid,midg 2.7446495E-08 -8.2957863E-09 1,midg,midg; igrid,midg,midg 2.4086413E-08 -7.9197832E-10 gauss-seidel spectral radius is 0.9875718 estimated iterations to convergence 73 setup time was (sec) 0.7200000 now iterating at: 14:14:04 rms-change max change #iterations 0.1530556 21.65387 at 10iterations 1.5413056E-02 2.097300 at 20iterations 1.5593150E-03 0.2320366 at 30iterations 1.5554257E-04 2.0952225E-02 at 40iterations 1.5902884E-05 2.4585724E-03 at 50iterations finished qdiffx linear iterations at : 14:14:08 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.5902884E-05 2.4585724E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 14:14:09 4.509u 0.413s 0:05.59 87.8% 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 14:14:09 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.937064 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 1.937064 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2456 net assigned charge : 6.488015 assigned positive charge : 392.9160 centred at (gu) : 89.60387 91.18087 94.19733 assigned negative charge : -386.4283 centred at (gu) : 89.87342 91.59612 94.53015 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 27997 mr = 51853 m= 4548 mr = 19595 m= 262 mr = 2527 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 35971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 19353 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) : 0.6456879 object centre at (A) : -100.4725 30.20950 54.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3079535E-02 -4.1924128E-03 midg,1,midg; midg,igrid,midg 4.7608819E-02 -2.6729390E-02 1,midg,midg; igrid,midg,midg 2.7561475E-02 -1.0827700E-02 gauss-seidel spectral radius is 0.9986827 estimated iterations to convergence 218 setup time was (sec) 1.130000 now iterating at: 14:14:11 rms-change max change #iterations 4.439996 200.6427 at 10iterations 2.100141 71.87878 at 20iterations 0.9985758 35.49590 at 30iterations 0.4733652 15.64047 at 40iterations 0.2242682 7.027646 at 50iterations 0.1063051 3.203705 at 60iterations 5.0653100E-02 1.567564 at 70iterations 2.3977529E-02 0.7843628 at 80iterations 1.1389938E-02 0.3710747 at 90iterations 5.4258974E-03 0.1864700 at 100iterations 2.5647657E-03 9.6454620E-02 at 110iterations 1.2208840E-03 3.7016630E-02 at 120iterations finished qdiffx linear iterations at : 14:14:20 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 1.2208840E-03 3.7016630E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 14:14:21 10.761u 0.472s 0:11.69 96.0% 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 14:14:21 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.905596 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): -123.9590 -76.98600 ymin,ymax (A): 2.642000 57.77700 zmin,zma (A): 28.81100 80.00800 x,y,z range (A): 46.97300 55.13500 51.19700 scale (grids/A): 2.905596 object centre (A): -100.4725 30.20950 54.40950 number of atom coordinates read : 2499 total number of charged atoms : 2456 net assigned charge : 6.488015 assigned positive charge : 392.9160 centred at (gu) : 89.40577 91.77116 96.29585 assigned negative charge : -386.4283 centred at (gu) : 89.81013 92.39413 96.79510 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 178322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 89959 mr = 126471 m= 32683 mr = 71564 m= 8063 mr = 24828 m= 1205 mr = 5590 m= 66 mr = 731 m= 0 mr = 17 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 81097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 19647 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) : 1.937064 object centre at (A) : -100.4725 30.20950 54.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3070830 -9.3582094E-02 midg,1,midg; midg,igrid,midg 0.5498632 -0.5440838 1,midg,midg; igrid,midg,midg 0.2336560 -0.1075243 gauss-seidel spectral radius is 0.9992862 estimated iterations to convergence 295 setup time was (sec) 2.530000 now iterating at: 14:14:24 rms-change max change #iterations 10.55347 374.0499 at 10iterations 6.340901 158.3330 at 20iterations 3.783336 91.25100 at 30iterations 2.242738 51.95682 at 40iterations 1.326184 31.55988 at 50iterations 0.7794179 15.44882 at 60iterations 0.4576513 9.473145 at 70iterations 0.2683583 5.193177 at 80iterations 0.1565850 2.929428 at 90iterations 9.1403559E-02 1.867020 at 100iterations 5.3397201E-02 1.023121 at 110iterations 3.1084089E-02 0.5775909 at 120iterations 1.8135509E-02 0.3575134 at 130iterations 1.0544722E-02 0.1840380 at 140iterations 6.1291032E-03 0.1103420 at 150iterations 3.5802480E-03 6.4275742E-02 at 160iterations 2.0873817E-03 4.3441772E-02 at 170iterations 1.2195422E-03 2.2449493E-02 at 180iterations finished qdiffx linear iterations at : 14:14:39 total time elapsed so far: 18.24000 # loops : 180 mean,max change (kT/e) : 1.2195422E-03 2.2449493E-02 energy calculations done at 18.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.46000 DelPhi exited at 14:14:40 18.460u 0.477s 0:19.28 98.1% 0+0k 0+0io 0pf+0w