Sat Oct 8 14:01:15 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 14:01:15 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6520266 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 0.6520266 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 88.94199 89.58736 91.91899 assigned negative charge : -450.1394 centred at (gu) : 88.95462 89.47089 91.84512 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8416 nv = 96 ne = 84 npr = 63313 no. pairs analyzed = 63313 no. exposed pairs = 3374 no. arc points = 23455 no. surface atoms = 1158 nbur = 1838 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4976 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3300000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0720226E-08 1.7321589E-08 midg,1,midg; midg,igrid,midg -2.6369660E-08 1.7495244E-08 1,midg,midg; igrid,midg,midg 1.6167012E-10 -3.6795862E-09 gauss-seidel spectral radius is 0.9878385 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 14:01:16 rms-change max change #iterations 0.1761589 23.37886 at 10iterations 1.8734677E-02 2.655449 at 20iterations 2.0048826E-03 0.2642899 at 30iterations 2.5448765E-04 3.0624390E-02 at 40iterations 4.3889890E-05 5.7430267E-03 at 50iterations finished qdiffx linear iterations at : 14:01:18 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.3889890E-05 5.7430267E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 14:01:19 3.127u 0.155s 0:03.55 92.1% 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 Sat Oct 8 2011 at 14:01:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.956080 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 1.956080 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 86.82532 88.76170 95.75655 assigned negative charge : -450.1394 centred at (gu) : 86.86359 88.41257 95.53489 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 91611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23455 grid for indexing accessible points = 1.400000 m= 34135 mr = 66526 m= 5443 mr = 25832 m= 393 mr = 3553 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 855 time to turn everything in is 0.6100000 number of dielectric boundary points 35540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22468 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) : 0.6520266 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1464258E-02 2.3460394E-02 midg,1,midg; midg,igrid,midg -1.6526405E-03 2.2045877E-02 1,midg,midg; igrid,midg,midg -4.2705636E-02 1.4583071E-03 gauss-seidel spectral radius is 0.9987313 estimated iterations to convergence 222 setup time was (sec) 0.8800000 now iterating at: 14:01:20 rms-change max change #iterations 4.870193 200.8053 at 10iterations 2.355800 74.68900 at 20iterations 1.134506 32.66984 at 30iterations 0.5480505 16.90939 at 40iterations 0.2638436 7.613457 at 50iterations 0.1269464 3.502889 at 60iterations 6.1269242E-02 1.998645 at 70iterations 2.9598607E-02 0.8192358 at 80iterations 1.4282698E-02 0.4257202 at 90iterations 6.9010803E-03 0.1982870 at 100iterations 3.3401786E-03 0.1010761 at 110iterations 1.6179401E-03 4.1560173E-02 at 120iterations finished qdiffx linear iterations at : 14:01:26 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 1.6179401E-03 4.1560173E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:01:26 6.995u 0.170s 0:07.42 96.4% 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 14:01:26 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.934120 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 2.934120 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 85.23785 88.14234 98.63457 assigned negative charge : -450.1394 centred at (gu) : 85.29537 87.61875 98.30231 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 211908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23455 grid for indexing accessible points = 1.400000 m= 110340 mr = 160187 m= 40461 mr = 92207 m= 10009 mr = 33164 m= 1554 mr = 7666 m= 105 mr = 1072 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 2951 time to turn everything in is 1.570000 number of dielectric boundary points 80039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 22791 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) : 1.956080 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3515815E-02 0.3446968 midg,1,midg; midg,igrid,midg -4.2346963E-03 0.2460551 1,midg,midg; igrid,midg,midg -0.6233829 0.2726240 gauss-seidel spectral radius is 0.9992867 estimated iterations to convergence 295 setup time was (sec) 1.840000 now iterating at: 14:01:28 rms-change max change #iterations 11.23035 368.4750 at 10iterations 6.598315 136.3974 at 20iterations 3.874286 80.91203 at 30iterations 2.267126 42.72377 at 40iterations 1.324517 23.67160 at 50iterations 0.7724743 14.30561 at 60iterations 0.4490948 7.464935 at 70iterations 0.2618947 4.644748 at 80iterations 0.1524151 2.429890 at 90iterations 8.8724375E-02 1.419132 at 100iterations 5.1658142E-02 0.8556719 at 110iterations 2.9985052E-02 0.4743428 at 120iterations 1.7461570E-02 0.2972953 at 130iterations 1.0132553E-02 0.1610098 at 140iterations 5.9167813E-03 9.7716808E-02 at 150iterations 3.4522070E-03 5.9162140E-02 at 160iterations 2.0266748E-03 3.2548904E-02 at 170iterations 1.1886716E-03 2.1348953E-02 at 180iterations finished qdiffx linear iterations at : 14:01:38 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.1886716E-03 2.1348953E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 14:01:38 11.624u 0.181s 0:12.06 97.8% 0+0k 0+0io 0pf+0w