Mon Oct 10 14:08:31 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 14:08:32 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 0.6477320 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 0.6477320 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 360.5432 centred at (gu) : 90.76785 91.05253 90.04040 assigned negative charge : -364.0438 centred at (gu) : 90.59107 90.96867 89.95738 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6713 nv = 96 ne = 84 npr = 48608 no. pairs analyzed = 48608 no. exposed pairs = 3031 no. arc points = 21290 no. surface atoms = 1028 nbur = 1343 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3602 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2008 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7771152E-08 4.4705626E-09 midg,1,midg; midg,igrid,midg -1.4454411E-08 5.8066862E-09 1,midg,midg; igrid,midg,midg -2.6247886E-08 1.9794356E-08 gauss-seidel spectral radius is 0.9876342 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 14:08:32 rms-change max change #iterations 0.1557206 22.61441 at 10iterations 1.5839724E-02 2.525541 at 20iterations 1.8800409E-03 0.2886906 at 30iterations 3.5041734E-04 5.5913925E-02 at 40iterations 9.3699608E-05 1.4997482E-02 at 50iterations finished qdiffx linear iterations at : 14:08:35 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 9.3699608E-05 1.4997482E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 14:08:36 3.505u 0.197s 0:04.04 91.3% 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 Mon Oct 10 2011 at 14:08:36 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 1.943196 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 1.943196 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 360.5432 centred at (gu) : 92.30322 93.15718 90.12078 assigned negative charge : -364.0438 centred at (gu) : 91.77317 92.90587 89.87221 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21290 grid for indexing accessible points = 1.400000 m= 26915 mr = 48735 m= 4834 mr = 19671 m= 368 mr = 3009 m= 5 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32182 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17642 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) : 0.6477320 object centre at (A) : -24.78650 -47.32750 -6.626000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5082216E-02 -8.7183844E-03 midg,1,midg; midg,igrid,midg -1.9772736E-02 4.9200177E-04 1,midg,midg; igrid,midg,midg -9.7930506E-03 3.9231583E-02 gauss-seidel spectral radius is 0.9986725 estimated iterations to convergence 217 setup time was (sec) 0.8600000 now iterating at: 14:08:37 rms-change max change #iterations 4.319445 168.8733 at 10iterations 2.033338 80.50603 at 20iterations 0.9662999 33.82464 at 30iterations 0.4562490 14.52098 at 40iterations 0.2154702 6.709238 at 50iterations 0.1021868 3.215337 at 60iterations 4.8412304E-02 1.518555 at 70iterations 2.3020770E-02 0.7721977 at 80iterations 1.0928083E-02 0.3395042 at 90iterations 5.2216775E-03 0.1927109 at 100iterations 2.5309001E-03 7.7911377E-02 at 110iterations 1.2371461E-03 3.9795160E-02 at 120iterations finished qdiffx linear iterations at : 14:08:43 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.2371461E-03 3.9795160E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:08:44 7.654u 0.213s 0:08.34 94.2% 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 14:08:44 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 2.914794 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 2.914794 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 360.5432 centred at (gu) : 93.45464 94.73566 90.18111 assigned negative charge : -364.0438 centred at (gu) : 92.65962 94.35889 89.80826 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21290 grid for indexing accessible points = 1.400000 m= 84545 mr = 118349 m= 33059 mr = 68539 m= 8913 mr = 26435 m= 1403 mr = 6514 m= 111 mr = 884 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 72573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 17900 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) : 1.943196 object centre at (A) : -24.78650 -47.32750 -6.626000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2104448 -0.2795764 midg,1,midg; midg,igrid,midg -0.1142093 8.3261296E-02 1,midg,midg; igrid,midg,midg 6.5408632E-02 0.5576527 gauss-seidel spectral radius is 0.9992663 estimated iterations to convergence 291 setup time was (sec) 1.750000 now iterating at: 14:08:46 rms-change max change #iterations 10.01495 512.9547 at 10iterations 5.870343 134.3509 at 20iterations 3.418347 64.43222 at 30iterations 1.982030 36.60823 at 40iterations 1.152404 21.27442 at 50iterations 0.6679590 12.11147 at 60iterations 0.3852548 8.421293 at 70iterations 0.2224942 4.143432 at 80iterations 0.1283673 2.327049 at 90iterations 7.3868774E-02 1.419483 at 100iterations 4.2653725E-02 0.7932968 at 110iterations 2.4575459E-02 0.4498329 at 120iterations 1.4187226E-02 0.2613676 at 130iterations 8.1840837E-03 0.1597176 at 140iterations 4.7348798E-03 8.1729889E-02 at 150iterations 2.7389757E-03 4.7581792E-02 at 160iterations 1.5943404E-03 2.9953003E-02 at 170iterations 9.3530066E-04 1.8085003E-02 at 180iterations finished qdiffx linear iterations at : 14:08:57 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 9.3530066E-04 1.8085003E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 14:08:58 12.800u 0.238s 0:13.48 96.6% 0+0k 0+0io 0pf+0w