Sat Oct 8 18:47:03 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 Sat Oct 8 2011 at 18:47:04 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 = 2534 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: 0.6248683 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): -32.22100 17.49100 ymin,ymax (A): -23.15400 23.31400 zmin,zma (A): -12.34200 44.63000 x,y,z range (A): 49.71200 46.46800 56.97200 scale (grids/A): 0.6248683 object centre (A): -7.365001 7.9999924E-02 16.14400 number of atom coordinates read : 2534 total number of charged atoms : 2394 net assigned charge : 3.000009 assigned positive charge : 380.3962 centred at (gu) : 88.66724 89.01257 89.61844 assigned negative charge : -377.3966 centred at (gu) : 88.60102 89.03921 89.46036 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6473 nv = 96 ne = 84 npr = 52979 no. pairs analyzed = 52979 no. exposed pairs = 2892 no. arc points = 20700 no. surface atoms = 980 nbur = 1554 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 3685 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2800000 number of dielectric boundary points 3113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.8409805E-09 1.3258939E-08 midg,1,midg; midg,igrid,midg 6.0423329E-09 7.6881973E-10 1,midg,midg; igrid,midg,midg -2.8142690E-09 5.8253913E-09 gauss-seidel spectral radius is 0.9867254 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 18:47:04 rms-change max change #iterations 0.1289313 22.70347 at 10iterations 1.2302352E-02 1.780727 at 20iterations 1.1453483E-03 0.1773758 at 30iterations 1.0835491E-04 1.7410278E-02 at 40iterations 1.0212749E-05 1.4305115E-03 at 50iterations finished qdiffx linear iterations at : 18:47:07 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.0212749E-05 1.4305115E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 18:47:07 3.250u 0.180s 0:03.72 92.2% 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 Sat Oct 8 2011 at 18:47:07 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 = 2534 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: 1.874605 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): -32.22100 17.49100 ymin,ymax (A): -23.15400 23.31400 zmin,zma (A): -12.34200 44.63000 x,y,z range (A): 49.71200 46.46800 56.97200 scale (grids/A): 1.874605 object centre (A): -7.365001 7.9999924E-02 16.14400 number of atom coordinates read : 2534 total number of charged atoms : 2394 net assigned charge : 3.000009 assigned positive charge : 380.3962 centred at (gu) : 86.00179 87.03741 88.85496 assigned negative charge : -377.3966 centred at (gu) : 85.80300 87.11746 88.38096 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 25665 mr = 49405 m= 3974 mr = 19351 m= 231 mr = 2542 m= 0 mr = 74 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 5543 time to turn everything in is 0.5100000 number of dielectric boundary points 28577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18772 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) : 0.6248683 object centre at (A) : -7.365001 7.9999924E-02 16.14400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4785299E-02 3.3249106E-02 midg,1,midg; midg,igrid,midg 1.0700814E-02 3.3084801E-04 1,midg,midg; igrid,midg,midg -3.8755476E-03 2.9580565E-02 gauss-seidel spectral radius is 0.9985791 estimated iterations to convergence 210 setup time was (sec) 0.7900000 now iterating at: 18:47:08 rms-change max change #iterations 3.998795 183.9443 at 10iterations 1.842157 64.89020 at 20iterations 0.8522779 27.85631 at 30iterations 0.3913875 14.46098 at 40iterations 0.1812468 5.819537 at 50iterations 8.3644092E-02 2.740561 at 60iterations 3.8654778E-02 1.322212 at 70iterations 1.7839402E-02 0.5725737 at 80iterations 8.2181487E-03 0.2630429 at 90iterations 3.8010019E-03 0.1154292 at 100iterations 1.7565611E-03 5.5000305E-02 at 110iterations 8.1264367E-04 2.6294708E-02 at 120iterations finished qdiffx linear iterations at : 18:47:15 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 8.1264367E-04 2.6294708E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 18:47:15 7.391u 0.215s 0:07.93 95.8% 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 18:47:15 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 = 2534 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.811908 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): -32.22100 17.49100 ymin,ymax (A): -23.15400 23.31400 zmin,zma (A): -12.34200 44.63000 x,y,z range (A): 49.71200 46.46800 56.97200 scale (grids/A): 2.811908 object centre (A): -7.365001 7.9999924E-02 16.14400 number of atom coordinates read : 2534 total number of charged atoms : 2394 net assigned charge : 3.000009 assigned positive charge : 380.3962 centred at (gu) : 84.00252 85.55613 88.28233 assigned negative charge : -377.3966 centred at (gu) : 83.70451 85.67607 87.57135 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 162040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 82999 mr = 119238 m= 30106 mr = 68995 m= 7240 mr = 24769 m= 983 mr = 5432 m= 54 mr = 671 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 18803 time to turn everything in is 1.220000 number of dielectric boundary points 64294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19146 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) : 1.874605 object centre at (A) : -7.365001 7.9999924E-02 16.14400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1511264 0.3589250 midg,1,midg; midg,igrid,midg 0.1362425 -2.4766959E-02 1,midg,midg; igrid,midg,midg -1.8366380E-02 0.3800237 gauss-seidel spectral radius is 0.9992355 estimated iterations to convergence 285 setup time was (sec) 1.540000 now iterating at: 18:47:17 rms-change max change #iterations 9.395075 339.3477 at 10iterations 5.397404 128.3422 at 20iterations 3.092577 66.84358 at 30iterations 1.765491 37.57821 at 40iterations 1.009231 21.37053 at 50iterations 0.5742083 10.43770 at 60iterations 0.3275434 7.021852 at 70iterations 0.1866161 3.790422 at 80iterations 0.1064586 1.954710 at 90iterations 6.0524423E-02 1.247828 at 100iterations 3.4365885E-02 0.7707167 at 110iterations 1.9621329E-02 0.3767443 at 120iterations 1.1170509E-02 0.2090187 at 130iterations 6.3483804E-03 0.1168445 at 140iterations 3.6113018E-03 6.9014549E-02 at 150iterations 2.0573239E-03 4.1458130E-02 at 160iterations 1.1715442E-03 2.4944305E-02 at 170iterations 6.6446664E-04 1.1796951E-02 at 180iterations finished qdiffx linear iterations at : 18:47:27 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 6.6446664E-04 1.1796951E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 18:47:28 11.821u 0.213s 0:12.30 97.8% 0+0k 0+0io 0pf+0w