Tue Nov 22 14:21:14 PST 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 Tue Nov 22 2011 at 14:21:18 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 = 1966 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: 0.5906655 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 0.5906655 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 289.0661 centred at (gu) : 90.51043 89.56112 89.49201 assigned negative charge : -288.0663 centred at (gu) : 90.44808 89.66031 89.48016 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4584 nv = 96 ne = 84 npr = 40361 no. pairs analyzed = 40361 no. exposed pairs = 2432 no. arc points = 16947 no. surface atoms = 823 nbur = 1143 mkacc time = 7.0000000E-02 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 = 1.456000 m= 219 mr = 2525 m= 0 mr = 15 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5642 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6107536E-11 4.8066301E-10 midg,1,midg; midg,igrid,midg 2.5262030E-09 -1.5560360E-09 1,midg,midg; igrid,midg,midg -8.5725560E-10 1.7458115E-09 gauss-seidel spectral radius is 0.9851167 estimated iterations to convergence 67 setup time was (sec) 0.3700000 now iterating at: 14:21:21 rms-change max change #iterations 8.9192785E-02 18.68921 at 10iterations 7.2290529E-03 1.308455 at 20iterations 5.7914230E-04 0.1029534 at 30iterations 4.6529127E-05 8.3789825E-03 at 40iterations 3.7890043E-06 7.3242188E-04 at 50iterations finished qdiffx linear iterations at : 14:21:30 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 3.7890043E-06 7.3242188E-04 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 14:21:31 3.691u 0.203s 0:14.59 26.6% 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 Tue Nov 22 2011 at 14:21:34 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 = 1966 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: 1.771996 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 1.771996 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 289.0661 centred at (gu) : 91.53107 88.68321 88.47598 assigned negative charge : -288.0663 centred at (gu) : 91.34455 88.98093 88.44055 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16947 grid for indexing accessible points = 1.400000 m= 17585 mr = 33601 m= 2328 mr = 13209 m= 108 mr = 1500 m= 0 mr = 43 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.2600000 number of dielectric boundary points 20956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14307 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) : 0.5906655 object centre at (A) : -12.69300 21.23100 28.57350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6436420E-02 1.9969914E-02 midg,1,midg; midg,igrid,midg -9.7524212E-04 -6.9457395E-03 1,midg,midg; igrid,midg,midg -2.7223490E-03 -6.1659608E-03 gauss-seidel spectral radius is 0.9983461 estimated iterations to convergence 195 setup time was (sec) 0.4900000 now iterating at: 14:21:38 rms-change max change #iterations 3.093554 158.9915 at 10iterations 1.333057 56.62497 at 20iterations 0.5827321 23.17851 at 30iterations 0.2519861 10.48385 at 40iterations 0.1090583 4.228348 at 50iterations 4.7384918E-02 1.840358 at 60iterations 2.0509910E-02 0.7646942 at 70iterations 8.9144083E-03 0.3312378 at 80iterations 3.8691030E-03 0.1468430 at 90iterations 1.6712231E-03 6.3524246E-02 at 100iterations 7.2598399E-04 2.8324127E-02 at 110iterations 3.1656693E-04 1.2598991E-02 at 120iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 3.1656693E-04 1.2598991E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 14:22:02 8.322u 0.240s 0:29.29 29.2% 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 Tue Nov 22 2011 at 14:22:04 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 = 1966 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: 2.657995 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 2.657995 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 289.0661 centred at (gu) : 92.29679 88.02489 87.71404 assigned negative charge : -288.0663 centred at (gu) : 92.01692 88.47157 87.66083 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 113983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16947 grid for indexing accessible points = 1.400000 m= 57065 mr = 81430 m= 20180 mr = 46996 m= 4157 mr = 16711 m= 488 mr = 3233 m= 19 mr = 343 m= 0 mr = 8 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 536 time to turn everything in is 0.6600000 number of dielectric boundary points 47171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14668 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) : 1.771996 object centre at (A) : -12.69300 21.23100 28.57350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2542758 0.1321962 midg,1,midg; midg,igrid,midg -4.1312441E-02 -0.1022248 1,midg,midg; igrid,midg,midg -5.4248266E-02 -0.1243571 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 0.9200000 now iterating at: 14:22:10 rms-change max change #iterations 7.497886 239.6107 at 10iterations 4.162025 115.4369 at 20iterations 2.314897 60.99165 at 30iterations 1.279941 31.07001 at 40iterations 0.7064387 16.23215 at 50iterations 0.3909098 8.516186 at 60iterations 0.2154909 5.126381 at 70iterations 0.1191050 2.583747 at 80iterations 6.5552406E-02 1.551765 at 90iterations 3.6220860E-02 0.8944912 at 100iterations 1.9885635E-02 0.4638302 at 110iterations 1.0987552E-02 0.2520142 at 120iterations 6.0878391E-03 0.1320477 at 130iterations 3.3542672E-03 7.2092891E-02 at 140iterations 1.8444309E-03 4.4063628E-02 at 150iterations 1.0198486E-03 2.2390485E-02 at 160iterations 5.6286773E-04 1.1614799E-02 at 170iterations 3.1047422E-04 7.0598125E-03 at 180iterations finished qdiffx linear iterations at : 14:22:41 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 3.1047422E-04 7.0598125E-03 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:22:43 13.393u 0.243s 0:38.92 35.0% 0+0k 0+0io 0pf+0w