Sun Oct 9 08:36:24 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 Sun Oct 9 2011 at 08:36:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6129 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4685999 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 0.4685999 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.985965 assigned positive charge : 926.9790 centred at (gu) : 89.91174 90.15029 90.35152 assigned negative charge : -929.9727 centred at (gu) : 89.85429 90.13388 90.45898 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8155 nv = 96 ne = 84 npr = 124240 no. pairs analyzed = 124240 no. exposed pairs = 7605 no. arc points = 52581 no. surface atoms = 2550 nbur = 3579 mkacc time = 0.2200000 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 = 1.820000 m= 237 mr = 4142 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 4248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4820 ## 914 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0913238E-11 -6.3620838E-11 midg,1,midg; midg,igrid,midg -1.2595345E-11 2.6699517E-12 1,midg,midg; igrid,midg,midg -3.3826462E-11 2.1398695E-11 gauss-seidel spectral radius is 0.9768234 estimated iterations to convergence 55 setup time was (sec) 0.6000000 now iterating at: 08:36:25 rms-change max change #iterations 4.9630709E-02 8.736694 at 10iterations 2.5991129E-03 0.4830093 at 20iterations 3.8300155E-04 9.6057892E-02 at 30iterations 9.6670097E-05 2.2628784E-02 at 40iterations 2.7021393E-05 5.6915283E-03 at 50iterations finished qdiffx linear iterations at : 08:36:28 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.7021393E-05 5.6915283E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 08:36:28 3.626u 0.182s 0:04.08 93.1% 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 Sun Oct 9 2011 at 08:36:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6129 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.405800 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 1.405800 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.985965 assigned positive charge : 926.9790 centred at (gu) : 89.73329 90.44900 91.05268 assigned negative charge : -929.9727 centred at (gu) : 89.56250 90.40128 91.37643 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 93971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 24473 mr = 63855 m= 1560 mr = 15631 m= 26 mr = 508 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1252 time to turn everything in is 0.4800000 number of dielectric boundary points 40036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 892 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 43246 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) : 0.4685999 object centre at (A) : 35.20350 4.468501 61.38300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0621370E-02 -3.1715969E-03 midg,1,midg; midg,igrid,midg -2.9894726E-03 -1.5459240E-03 1,midg,midg; igrid,midg,midg -7.2090048E-03 -1.1895150E-02 gauss-seidel spectral radius is 0.9978322 estimated iterations to convergence 171 setup time was (sec) 0.7100000 now iterating at: 08:36:29 rms-change max change #iterations 3.590182 151.1951 at 10iterations 1.378596 43.86682 at 20iterations 0.5311851 16.68203 at 30iterations 0.2047073 6.713295 at 40iterations 7.9010434E-02 2.567894 at 50iterations 3.0465972E-02 1.032185 at 60iterations 1.1792818E-02 0.3686581 at 70iterations 4.5999936E-03 0.1629257 at 80iterations 1.7977357E-03 5.7853699E-02 at 90iterations 7.1857555E-04 2.5001526E-02 at 100iterations 3.0218388E-04 1.1558533E-02 at 110iterations 1.3720428E-04 5.8460236E-03 at 120iterations finished qdiffx linear iterations at : 08:36:36 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.3720428E-04 5.8460236E-03 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 08:36:37 8.009u 0.217s 0:08.53 96.2% 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 Sun Oct 9 2011 at 08:36:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6129 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.108700 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): -2.782000 73.18900 ymin,ymax (A): -27.77300 36.71000 zmin,zma (A): 30.30900 92.45700 x,y,z range (A): 75.97099 64.48300 62.14800 scale (grids/A): 2.108700 object centre (A): 35.20350 4.468501 61.38300 number of atom coordinates read : 6129 total number of charged atoms : 5960 net assigned charge : -2.985965 assigned positive charge : 926.9790 centred at (gu) : 89.59927 90.67287 91.57837 assigned negative charge : -929.9727 centred at (gu) : 89.34380 90.60178 92.06461 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 220205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 91440 mr = 158215 m= 19352 mr = 69641 m= 1904 mr = 13457 m= 53 mr = 969 m= 0 mr = 7 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 4243 time to turn everything in is 1.110000 number of dielectric boundary points 90665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 47343 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) : 1.405800 object centre at (A) : 35.20350 4.468501 61.38300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2085001 -7.8205988E-02 midg,1,midg; midg,igrid,midg -5.3498149E-02 -2.8237913E-02 1,midg,midg; igrid,midg,midg -0.1000423 -0.5206547 gauss-seidel spectral radius is 0.9991090 estimated iterations to convergence 265 setup time was (sec) 1.360000 now iterating at: 08:36:38 rms-change max change #iterations 10.31426 341.6017 at 10iterations 5.826140 135.1249 at 20iterations 3.278681 74.07716 at 30iterations 1.830863 36.81279 at 40iterations 1.018475 22.03974 at 50iterations 0.5639937 11.41085 at 60iterations 0.3126624 6.108681 at 70iterations 0.1725202 3.533436 at 80iterations 9.5272459E-02 2.049326 at 90iterations 5.2280281E-02 1.032545 at 100iterations 2.8829230E-02 0.6076398 at 110iterations 1.5839517E-02 0.3116570 at 120iterations 8.6957347E-03 0.1731062 at 130iterations 4.7760899E-03 9.1018677E-02 at 140iterations 2.6218898E-03 5.0230265E-02 at 150iterations 1.4428971E-03 2.9229164E-02 at 160iterations 7.9635280E-04 1.5510559E-02 at 170iterations 4.4045909E-04 8.1448555E-03 at 180iterations finished qdiffx linear iterations at : 08:36:51 total time elapsed so far: 14.31000 # loops : 180 mean,max change (kT/e) : 4.4045909E-04 8.1448555E-03 energy calculations done at 14.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.45000 DelPhi exited at 08:36:52 14.452u 0.227s 0:14.99 97.8% 0+0k 0+0io 0pf+0w