Mon Oct 10 22:03:50 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 22:03:50 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 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: 0.5608596 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 0.5608596 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 417.9342 centred at (gu) : 92.12856 89.29773 90.75838 assigned negative charge : -417.4355 centred at (gu) : 92.04553 89.33427 90.69043 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5923 nv = 96 ne = 84 npr = 55446 no. pairs analyzed = 55446 no. exposed pairs = 3849 no. arc points = 27200 no. surface atoms = 1293 nbur = 1531 mkacc time = 0.1500000 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 = 1.540000 m= 248 mr = 2927 m= 1 mr = 11 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 0.3100000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2743 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8587407E-10 8.9561958E-10 midg,1,midg; midg,igrid,midg 4.9019300E-10 -3.0838615E-10 1,midg,midg; igrid,midg,midg -5.1791055E-10 1.5281970E-09 gauss-seidel spectral radius is 0.9835997 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 22:03:51 rms-change max change #iterations 7.7288896E-02 12.02512 at 10iterations 5.5729854E-03 0.8045807 at 20iterations 4.3806015E-04 7.1954727E-02 at 30iterations 4.1069619E-05 7.7915192E-03 at 40iterations 5.4414058E-06 7.5149536E-04 at 50iterations finished qdiffx linear iterations at : 22:03:54 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 5.4414058E-06 7.5149536E-04 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 22:03:55 4.474u 0.387s 0:05.18 93.6% 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 22:03:55 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 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: 1.682579 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 1.682579 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 417.9342 centred at (gu) : 96.38471 87.89227 92.27454 assigned negative charge : -417.4355 centred at (gu) : 96.13644 88.00265 92.07118 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19889 mr = 42812 m= 2401 mr = 13459 m= 67 mr = 1224 m= 0 mr = 6 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 80 time to turn everything in is 0.5400000 number of dielectric boundary points 30152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21132 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) : 0.5608596 object centre at (A) : -0.7869997 -5.173999 25.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5030170E-02 1.1024320E-02 midg,1,midg; midg,igrid,midg -3.0482037E-03 -9.1907382E-03 1,midg,midg; igrid,midg,midg -2.8541539E-04 2.4197582E-02 gauss-seidel spectral radius is 0.9982880 estimated iterations to convergence 192 setup time was (sec) 0.8400000 now iterating at: 22:03:56 rms-change max change #iterations 3.403087 169.3467 at 10iterations 1.449399 61.97916 at 20iterations 0.6190421 22.86906 at 30iterations 0.2638935 9.779129 at 40iterations 0.1128302 3.977840 at 50iterations 4.8247479E-02 1.834174 at 60iterations 2.0570271E-02 0.7235165 at 70iterations 8.7796291E-03 0.3059053 at 80iterations 3.7733552E-03 0.1391258 at 90iterations 1.6120821E-03 6.1820984E-02 at 100iterations 6.8925007E-04 2.6260376E-02 at 110iterations 2.9518668E-04 1.0192871E-02 at 120iterations finished qdiffx linear iterations at : 22:04:06 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 2.9518668E-04 1.0192871E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.49000 DelPhi exited at 22:04:06 10.496u 0.426s 0:11.45 95.2% 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 22:04:06 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.523868 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): -26.86300 25.28900 ymin,ymax (A): -33.67800 23.33000 zmin,zma (A): -6.271000 57.20300 x,y,z range (A): 52.15200 57.00800 63.47400 scale (grids/A): 2.523868 object centre (A): -0.7869997 -5.173999 25.46600 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.5000103 assigned positive charge : 417.9342 centred at (gu) : 99.57684 86.83821 93.41164 assigned negative charge : -417.4355 centred at (gu) : 99.20457 87.00391 93.10667 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 151539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27200 grid for indexing accessible points = 1.400000 m= 67465 mr = 105174 m= 20574 mr = 52240 m= 3751 mr = 15356 m= 277 mr = 2585 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 290 time to turn everything in is 1.330000 number of dielectric boundary points 68135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 21884 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) : 1.682579 object centre at (A) : -0.7869997 -5.173999 25.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5649900 0.2028063 midg,1,midg; midg,igrid,midg -6.7571670E-02 -0.1290264 1,midg,midg; igrid,midg,midg -1.9948799E-02 0.3290217 gauss-seidel spectral radius is 0.9991720 estimated iterations to convergence 274 setup time was (sec) 1.650000 now iterating at: 22:04:08 rms-change max change #iterations 8.755163 432.5643 at 10iterations 4.986079 121.0455 at 20iterations 2.823970 65.16109 at 30iterations 1.591504 32.24398 at 40iterations 0.8925130 22.28111 at 50iterations 0.4998278 10.89542 at 60iterations 0.2788636 6.545012 at 70iterations 0.1560596 3.276260 at 80iterations 8.6798660E-02 1.861624 at 90iterations 4.8468545E-02 1.008025 at 100iterations 2.6960483E-02 0.5805893 at 110iterations 1.5016784E-02 0.3180275 at 120iterations 8.3604306E-03 0.1735945 at 130iterations 4.6481043E-03 0.1007462 at 140iterations 2.5902062E-03 5.1821947E-02 at 150iterations 1.4405119E-03 2.9579163E-02 at 160iterations 8.0347114E-04 1.7395020E-02 at 170iterations 4.4745690E-04 8.5144043E-03 at 180iterations finished qdiffx linear iterations at : 22:04:24 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 4.4745690E-04 8.5144043E-03 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.72000 DelPhi exited at 22:04:25 17.721u 0.459s 0:18.85 96.3% 0+0k 0+0io 0pf+0w