Mon Oct 10 17:00:28 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 Mon Oct 10 2011 at 17:00:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3445 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: 0.6430520 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 0.6430520 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 528.5495 centred at (gu) : 89.31533 91.00377 89.47766 assigned negative charge : -525.5507 centred at (gu) : 89.34769 90.96250 89.54239 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9455 nv = 96 ne = 84 npr = 71262 no. pairs analyzed = 71262 no. exposed pairs = 3743 no. arc points = 25972 no. surface atoms = 1263 nbur = 2182 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 543 mr = 5709 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.2500000 number of dielectric boundary points 4217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 11506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7439522E-08 -5.8637006E-09 midg,1,midg; midg,igrid,midg -1.9901987E-09 1.4398157E-08 1,midg,midg; igrid,midg,midg 1.1685675E-08 -8.1971641E-10 gauss-seidel spectral radius is 0.9875329 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 17:00:29 rms-change max change #iterations 0.1761183 22.02752 at 10iterations 1.8248275E-02 2.380204 at 20iterations 2.1521107E-03 0.2718468 at 30iterations 5.0560350E-04 5.3855896E-02 at 40iterations 1.9898389E-04 2.2891998E-02 at 50iterations finished qdiffx linear iterations at : 17:00:32 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 1.9898389E-04 2.2891998E-02 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 17:00:33 3.885u 0.186s 0:04.63 87.6% 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 Mon Oct 10 2011 at 17:00:33 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 = 3445 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: 1.929156 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 1.929156 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 528.5495 centred at (gu) : 87.94517 93.01059 88.43220 assigned negative charge : -525.5507 centred at (gu) : 88.04257 92.88696 88.62663 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 102302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25972 grid for indexing accessible points = 1.400000 m= 40033 mr = 75302 m= 6707 mr = 30952 m= 460 mr = 4336 m= 5 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2229 time to turn everything in is 0.4900000 number of dielectric boundary points 38715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 25939 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) : 0.6430520 object centre at (A) : 37.47650 -15.63050 57.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3252714E-02 -1.3883970E-02 midg,1,midg; midg,igrid,midg -7.7984454E-03 2.5983380E-02 1,midg,midg; igrid,midg,midg 2.4193484E-02 4.1976955E-02 gauss-seidel spectral radius is 0.9987344 estimated iterations to convergence 223 setup time was (sec) 0.7300000 now iterating at: 17:00:34 rms-change max change #iterations 5.180819 175.4424 at 10iterations 2.512593 78.80348 at 20iterations 1.215963 34.82670 at 30iterations 0.5891255 16.23351 at 40iterations 0.2849513 9.040677 at 50iterations 0.1377738 3.888516 at 60iterations 6.6894397E-02 1.842403 at 70iterations 3.2407053E-02 0.8664629 at 80iterations 1.5725972E-02 0.4088364 at 90iterations 7.7183899E-03 0.2005157 at 100iterations 3.8322159E-03 0.1032238 at 110iterations 1.9748253E-03 5.4462433E-02 at 120iterations finished qdiffx linear iterations at : 17:00:41 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 1.9748253E-03 5.4462433E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 17:00:42 8.551u 0.238s 0:09.33 94.1% 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 Mon Oct 10 2011 at 17:00:42 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 = 3445 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: 2.893734 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 2.893734 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 528.5495 centred at (gu) : 86.91747 94.51559 87.64802 assigned negative charge : -525.5507 centred at (gu) : 87.06363 94.33038 87.93982 start vw surface at 0.1000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 236420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25972 grid for indexing accessible points = 1.400000 m= 128220 mr = 180929 m= 48569 mr = 108359 m= 12206 mr = 40143 m= 1957 mr = 9288 m= 165 mr = 1350 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 7567 time to turn everything in is 1.340000 number of dielectric boundary points 87372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 26376 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) : 1.929156 object centre at (A) : 37.47650 -15.63050 57.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4328205 -3.4204584E-02 midg,1,midg; midg,igrid,midg -5.0464861E-02 0.3330884 1,midg,midg; igrid,midg,midg 0.3035494 0.5427887 gauss-seidel spectral radius is 0.9992919 estimated iterations to convergence 297 setup time was (sec) 1.600000 now iterating at: 17:00:44 rms-change max change #iterations 11.94120 391.7827 at 10iterations 7.092286 144.5331 at 20iterations 4.192944 80.53886 at 30iterations 2.474030 42.32230 at 40iterations 1.455826 27.62037 at 50iterations 0.8556424 14.76942 at 60iterations 0.5010514 9.071650 at 70iterations 0.2945512 4.565136 at 80iterations 0.1718373 3.093565 at 90iterations 0.1005098 1.767126 at 100iterations 5.8868092E-02 0.8758011 at 110iterations 3.4387346E-02 0.5032959 at 120iterations 2.0093998E-02 0.3185158 at 130iterations 1.1726555E-02 0.1764832 at 140iterations 6.8782484E-03 0.1089935 at 150iterations 4.0303492E-03 6.0094357E-02 at 160iterations 2.3650336E-03 3.7021637E-02 at 170iterations 1.3980048E-03 2.1690369E-02 at 180iterations finished qdiffx linear iterations at : 17:00:56 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 1.3980048E-03 2.1690369E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 17:00:57 14.090u 0.278s 0:14.99 95.7% 0+0k 0+0io 0pf+0w