Sat Oct 8 16:24:26 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 Sat Oct 8 2011 at 16:24:26 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2426 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 0.6597235 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 0.6597235 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2363 net assigned charge : 1.806004 assigned positive charge : 367.1909 centred at (gu) : 88.95840 91.00183 90.46877 assigned negative charge : -365.3858 centred at (gu) : 88.92284 90.81705 90.57545 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7226 nv = 96 ne = 84 npr = 48001 no. pairs analyzed = 48001 no. exposed pairs = 3135 no. arc points = 21270 no. surface atoms = 1071 nbur = 1355 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4020 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2100 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1631328E-08 -1.7191295E-08 midg,1,midg; midg,igrid,midg -2.4555201E-08 4.6807724E-08 1,midg,midg; igrid,midg,midg -2.8217286E-09 8.8187866E-09 gauss-seidel spectral radius is 0.9880794 estimated iterations to convergence 75 setup time was (sec) 0.4900000 now iterating at: 16:24:27 rms-change max change #iterations 0.1621614 26.14243 at 10iterations 1.6965616E-02 2.409567 at 20iterations 1.8941101E-03 0.2424259 at 30iterations 2.7333695E-04 3.6242008E-02 at 40iterations 6.6449764E-05 9.3026161E-03 at 50iterations finished qdiffx linear iterations at : 16:24:29 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.6449764E-05 9.3026161E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 16:24:30 3.130u 0.163s 0:03.59 91.6% 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 Sat Oct 8 2011 at 16:24:30 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2426 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 1.979171 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 1.979171 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2363 net assigned charge : 1.806004 assigned positive charge : 367.1909 centred at (gu) : 86.87491 93.00490 91.40590 assigned negative charge : -365.3858 centred at (gu) : 86.76823 92.45085 91.72624 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 77680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21270 grid for indexing accessible points = 1.400000 m= 29020 mr = 54286 m= 5554 mr = 21584 m= 450 mr = 3834 m= 9 mr = 226 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.5400000 number of dielectric boundary points 32781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18657 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) : 0.6597235 object centre at (A) : 6.046000 27.01700 9.902999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6722394E-02 -1.9375846E-02 midg,1,midg; midg,igrid,midg -1.0201873E-02 2.6406046E-02 1,midg,midg; igrid,midg,midg -4.0549390E-02 4.0915846E-03 gauss-seidel spectral radius is 0.9987191 estimated iterations to convergence 221 setup time was (sec) 0.8100000 now iterating at: 16:24:31 rms-change max change #iterations 4.477719 219.4518 at 10iterations 2.142498 75.93230 at 20iterations 1.026622 33.00478 at 30iterations 0.4935308 16.96580 at 40iterations 0.2380908 7.892972 at 50iterations 0.1138253 3.476415 at 60iterations 5.4816768E-02 1.656788 at 70iterations 2.6320428E-02 0.7695427 at 80iterations 1.2683772E-02 0.3757496 at 90iterations 6.1051897E-03 0.2030048 at 100iterations 2.9424913E-03 9.0530872E-02 at 110iterations 1.4222533E-03 4.2068005E-02 at 120iterations finished qdiffx linear iterations at : 16:24:36 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.4222533E-03 4.2068005E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 16:24:37 6.973u 0.180s 0:07.45 95.9% 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 Sat Oct 8 2011 at 16:24:37 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2426 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 2.968756 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): -18.23200 30.32400 ymin,ymax (A): 3.827000 50.20700 zmin,zma (A): -17.07800 36.88400 x,y,z range (A): 48.55600 46.38000 53.96200 scale (grids/A): 2.968756 object centre (A): 6.046000 27.01700 9.902999 number of atom coordinates read : 2426 total number of charged atoms : 2363 net assigned charge : 1.806004 assigned positive charge : 367.1909 centred at (gu) : 85.31219 94.50718 92.10867 assigned negative charge : -365.3858 centred at (gu) : 85.15234 93.67621 92.58933 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 179692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21270 grid for indexing accessible points = 1.400000 m= 91342 mr = 131413 m= 35886 mr = 74909 m= 10526 mr = 29441 m= 2063 mr = 8286 m= 207 mr = 1598 m= 7 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 631 time to turn everything in is 1.380000 number of dielectric boundary points 73953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 18904 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) : 1.979171 object centre at (A) : 6.046000 27.01700 9.902999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2312091 -0.2455474 midg,1,midg; midg,igrid,midg -0.1140416 0.1748463 1,midg,midg; igrid,midg,midg -0.5464975 6.8345986E-02 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 1.650000 now iterating at: 16:24:39 rms-change max change #iterations 10.42362 409.1252 at 10iterations 6.169362 156.3345 at 20iterations 3.640197 82.07522 at 30iterations 2.142122 44.14686 at 40iterations 1.254303 23.76837 at 50iterations 0.7349186 15.01911 at 60iterations 0.4296642 7.579340 at 70iterations 0.2504895 4.525916 at 80iterations 0.1460720 2.439609 at 90iterations 8.5055187E-02 1.571178 at 100iterations 4.9610712E-02 0.8536911 at 110iterations 2.8794520E-02 0.4865456 at 120iterations 1.6731912E-02 0.2884445 at 130iterations 9.7334413E-03 0.1656837 at 140iterations 5.6575341E-03 0.1031303 at 150iterations 3.2862150E-03 5.7185173E-02 at 160iterations 1.9102099E-03 3.2287598E-02 at 170iterations 1.1145504E-03 2.2298813E-02 at 180iterations finished qdiffx linear iterations at : 16:24:48 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 1.1145504E-03 2.2298813E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 16:24:49 11.307u 0.188s 0:11.78 97.4% 0+0k 0+0io 0pf+0w