Sun Oct 9 10:28:26 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+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 Sun Oct 9 2011 at 10:28:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 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: 0.6223776 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 0.6223776 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.500015 assigned positive charge : 321.1405 centred at (gu) : 90.19172 90.67448 91.06353 assigned negative charge : -318.6413 centred at (gu) : 90.21605 90.52256 91.06262 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5866 nv = 96 ne = 84 npr = 43994 no. pairs analyzed = 43994 no. exposed pairs = 2989 no. arc points = 21477 no. surface atoms = 996 nbur = 1220 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 2965 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2700000 number of dielectric boundary points 3196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2129 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6395401E-09 2.7051636E-09 midg,1,midg; midg,igrid,midg -5.9400427E-09 1.2577137E-08 1,midg,midg; igrid,midg,midg 3.3771010E-09 7.0289546E-10 gauss-seidel spectral radius is 0.9866078 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 10:28:26 rms-change max change #iterations 0.1161313 21.24316 at 10iterations 1.0489019E-02 1.528540 at 20iterations 9.6072210E-04 0.1489506 at 30iterations 8.9681940E-05 1.4328003E-02 at 40iterations 8.2712522E-06 1.4474392E-03 at 50iterations finished qdiffx linear iterations at : 10:28:29 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 8.2712522E-06 1.4474392E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 10:28:30 3.292u 0.174s 0:03.82 90.5% 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 Sun Oct 9 2011 at 10:28:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 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: 1.867133 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 1.867133 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.500015 assigned positive charge : 321.1405 centred at (gu) : 90.57478 92.02312 93.19034 assigned negative charge : -318.6413 centred at (gu) : 90.64835 91.56785 93.18808 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21477 grid for indexing accessible points = 1.400000 m= 21266 mr = 41495 m= 3388 mr = 15023 m= 225 mr = 2120 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 467 time to turn everything in is 0.4700000 number of dielectric boundary points 29457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 16319 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) : 0.6223776 object centre at (A) : 23.97000 2.424001 21.22250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3735089E-02 3.4518626E-02 midg,1,midg; midg,igrid,midg -5.3882138E-03 2.7575430E-02 1,midg,midg; igrid,midg,midg -9.8843072E-03 -1.0309460E-02 gauss-seidel spectral radius is 0.9985549 estimated iterations to convergence 209 setup time was (sec) 0.7500000 now iterating at: 10:28:31 rms-change max change #iterations 3.642412 162.5808 at 10iterations 1.666566 72.05271 at 20iterations 0.7632527 26.26085 at 30iterations 0.3481958 13.85943 at 40iterations 0.1592252 7.253573 at 50iterations 7.3178075E-02 2.453803 at 60iterations 3.3400770E-02 1.230707 at 70iterations 1.5312496E-02 0.5662313 at 80iterations 7.0112967E-03 0.2504005 at 90iterations 3.2139721E-03 0.1265039 at 100iterations 1.4745034E-03 5.6188464E-02 at 110iterations 6.7101122E-04 2.1755219E-02 at 120iterations finished qdiffx linear iterations at : 10:28:37 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 6.7101122E-04 2.1755219E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 10:28:38 7.346u 0.213s 0:07.92 95.3% 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 Sun Oct 9 2011 at 10:28:38 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 = 2216 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: 2.800699 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 2.800699 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.500015 assigned positive charge : 321.1405 centred at (gu) : 90.86214 93.03471 94.78548 assigned negative charge : -318.6413 centred at (gu) : 90.97260 92.35181 94.78230 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 146291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21477 grid for indexing accessible points = 1.400000 m= 68932 mr = 101416 m= 24698 mr = 54608 m= 6208 mr = 19462 m= 936 mr = 4668 m= 57 mr = 601 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1534 time to turn everything in is 1.140000 number of dielectric boundary points 66352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 16627 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) : 1.867133 object centre at (A) : 23.97000 2.424001 21.22250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2218146 0.4508793 midg,1,midg; midg,igrid,midg -7.9589128E-02 0.2391028 1,midg,midg; igrid,midg,midg -0.1776784 -0.1406240 gauss-seidel spectral radius is 0.9992351 estimated iterations to convergence 285 setup time was (sec) 1.430000 now iterating at: 10:28:39 rms-change max change #iterations 8.603191 341.1389 at 10iterations 4.953621 132.5710 at 20iterations 2.840480 64.57324 at 30iterations 1.627208 33.34360 at 40iterations 0.9259168 18.91843 at 50iterations 0.5292411 11.06551 at 60iterations 0.3010758 6.171700 at 70iterations 0.1715839 3.990760 at 80iterations 9.7779520E-02 2.110584 at 90iterations 5.5531636E-02 1.093083 at 100iterations 3.1618126E-02 0.6219797 at 110iterations 1.7966501E-02 0.3613253 at 120iterations 1.0221871E-02 0.2047806 at 130iterations 5.8146059E-03 0.1117781 at 140iterations 3.3121898E-03 6.2631130E-02 at 150iterations 1.8827808E-03 3.4589648E-02 at 160iterations 1.0717885E-03 2.3124695E-02 at 170iterations 6.0982135E-04 1.2379169E-02 at 180iterations finished qdiffx linear iterations at : 10:28:49 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 6.0982135E-04 1.2379169E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 10:28:50 11.754u 0.225s 0:12.30 97.3% 0+0k 0+0io 0pf+0w