Mon Oct 10 09:16:18 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 Mon Oct 10 2011 at 09:16:18 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 = 1044 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: 0.7400939 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 0.7400939 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 144.4621 centred at (gu) : 91.81414 91.50282 91.47231 assigned negative charge : -142.9620 centred at (gu) : 91.65581 91.61819 91.13596 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4144 nv = 96 ne = 84 npr = 20593 no. pairs analyzed = 20593 no. exposed pairs = 1542 no. arc points = 11491 no. surface atoms = 520 nbur = 524 mkacc time = 5.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 1980 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 6.0000010E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 857 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 3942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0035967E-07 2.2633508E-07 midg,1,midg; midg,igrid,midg 5.6815562E-08 -3.9587974E-08 1,midg,midg; igrid,midg,midg -3.4322618E-08 1.3288799E-07 gauss-seidel spectral radius is 0.9903854 estimated iterations to convergence 83 setup time was (sec) 0.3900000 now iterating at: 09:16:18 rms-change max change #iterations 0.1587989 33.27590 at 10iterations 2.0874355E-02 4.208527 at 20iterations 2.7333307E-03 0.4446411 at 30iterations 3.6078453E-04 6.1888158E-02 at 40iterations 4.7445221E-05 7.9650879E-03 at 50iterations finished qdiffx linear iterations at : 09:16:21 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 4.7445221E-05 7.9650879E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.000000 DelPhi exited at 09:16:21 3.005u 0.205s 0:03.51 91.1% 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 Mon Oct 10 2011 at 09:16:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 2.220282 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 2.220282 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 144.4621 centred at (gu) : 95.44263 94.50855 94.41705 assigned negative charge : -142.9620 centred at (gu) : 94.96734 94.85461 93.40800 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 42515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11491 grid for indexing accessible points = 1.400000 m= 16132 mr = 26324 m= 3569 mr = 11637 m= 335 mr = 2352 m= 13 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 22139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7317 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) : 0.7400939 object centre at (A) : -8.534500 21.31000 35.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3942257E-03 4.6562210E-02 midg,1,midg; midg,igrid,midg 1.1341129E-02 1.2830500E-02 1,midg,midg; igrid,midg,midg -7.7673299E-03 1.3261077E-03 gauss-seidel spectral radius is 0.9988290 estimated iterations to convergence 231 setup time was (sec) 0.6500000 now iterating at: 09:16:22 rms-change max change #iterations 3.303588 236.1193 at 10iterations 1.615801 79.03033 at 20iterations 0.7976064 35.37986 at 30iterations 0.3934189 16.11923 at 40iterations 0.1939305 7.972342 at 50iterations 9.5486172E-02 3.829023 at 60iterations 4.7092192E-02 1.839985 at 70iterations 2.3255138E-02 0.8909130 at 80iterations 1.1438712E-02 0.4185219 at 90iterations 5.6703715E-03 0.2229815 at 100iterations 2.7901384E-03 0.1145554 at 110iterations 1.3834666E-03 5.6919098E-02 at 120iterations finished qdiffx linear iterations at : 09:16:28 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.3834666E-03 5.6919098E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 09:16:29 7.078u 0.247s 0:07.72 94.6% 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 09:16:29 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 = 1044 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: 3.330423 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 3.330423 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 144.4621 centred at (gu) : 98.16395 96.76278 96.62563 assigned negative charge : -142.9620 centred at (gu) : 97.45103 97.28192 95.11191 start vw surface at 0.1000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 97375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11491 grid for indexing accessible points = 1.400000 m= 48792 mr = 63700 m= 21066 mr = 38835 m= 6842 mr = 16943 m= 1416 mr = 5243 m= 120 mr = 922 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 49927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 7344 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) : 2.220282 object centre at (A) : -8.534500 21.31000 35.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3364689E-03 0.2748575 midg,1,midg; midg,igrid,midg 6.8758324E-02 0.1031685 1,midg,midg; igrid,midg,midg -2.8786287E-02 -1.7865915E-02 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.310000 now iterating at: 09:16:31 rms-change max change #iterations 7.385317 289.7437 at 10iterations 4.341665 126.7513 at 20iterations 2.544102 68.41620 at 30iterations 1.486480 42.37867 at 40iterations 0.8679258 21.08166 at 50iterations 0.5043502 12.72930 at 60iterations 0.2929570 7.083252 at 70iterations 0.1704518 4.121657 at 80iterations 9.9065870E-02 2.244877 at 90iterations 5.7557236E-02 1.350636 at 100iterations 3.3407845E-02 0.7942677 at 110iterations 1.9436484E-02 0.4330249 at 120iterations 1.1236658E-02 0.2642674 at 130iterations 6.5318104E-03 0.1444366 at 140iterations 3.7890901E-03 8.2580566E-02 at 150iterations 2.2066885E-03 4.9907684E-02 at 160iterations 1.2776327E-03 2.8158665E-02 at 170iterations 7.4428506E-04 1.5100479E-02 at 180iterations finished qdiffx linear iterations at : 09:16:40 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 7.4428506E-04 1.5100479E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 09:16:41 11.096u 0.255s 0:11.65 97.3% 0+0k 0+0io 0pf+0w