Sat Oct 15 13:46:07 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 15 2011 at 13:46:07 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 = 2279 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6383131 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): -18.42200 27.26100 ymin,ymax (A): -26.86400 28.90800 zmin,zma (A): -0.7110000 48.05900 x,y,z range (A): 45.68300 55.77200 48.77000 scale (grids/A): 0.6383131 object centre (A): 4.419499 1.022000 23.67400 number of atom coordinates read : 2279 total number of charged atoms : 2200 net assigned charge : -2.999997 assigned positive charge : 334.1343 centred at (gu) : 89.59970 90.27602 88.24044 assigned negative charge : -337.1349 centred at (gu) : 89.54935 90.24720 88.16591 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6288 nv = 96 ne = 84 npr = 46030 no. pairs analyzed = 46030 no. exposed pairs = 2999 no. arc points = 20742 no. surface atoms = 1022 nbur = 1257 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3355 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1800000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1985 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7585 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6451100E-08 2.0878148E-09 midg,1,midg; midg,igrid,midg -6.3905810E-09 -1.2792989E-09 1,midg,midg; igrid,midg,midg -9.6614228E-09 7.5260254E-10 gauss-seidel spectral radius is 0.9872599 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 13:46:08 rms-change max change #iterations 0.1326115 21.19194 at 10iterations 1.2933221E-02 2.003965 at 20iterations 1.3090312E-03 0.1765308 at 30iterations 1.4335586E-04 2.1664619E-02 at 40iterations 2.2004742E-05 3.0174255E-03 at 50iterations finished qdiffx linear iterations at : 13:46:11 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 2.2004742E-05 3.0174255E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 13:46:11 3.896u 0.255s 0:04.44 93.2% 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 15 2011 at 13:46:11 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 = 2279 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.914939 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): -18.42200 27.26100 ymin,ymax (A): -26.86400 28.90800 zmin,zma (A): -0.7110000 48.05900 x,y,z range (A): 45.68300 55.77200 48.77000 scale (grids/A): 1.914939 object centre (A): 4.419499 1.022000 23.67400 number of atom coordinates read : 2279 total number of charged atoms : 2200 net assigned charge : -2.999997 assigned positive charge : 334.1343 centred at (gu) : 88.79847 90.82771 84.72086 assigned negative charge : -337.1349 centred at (gu) : 88.64796 90.74161 84.49757 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20742 grid for indexing accessible points = 1.400000 m= 24123 mr = 46812 m= 3911 mr = 17253 m= 264 mr = 2363 m= 4 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 0.3500000 number of dielectric boundary points 29981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17319 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) : 0.6383131 object centre at (A) : 4.419499 1.022000 23.67400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8530294E-02 1.1088110E-02 midg,1,midg; midg,igrid,midg -6.0756351E-03 3.0502835E-02 1,midg,midg; igrid,midg,midg -3.1259891E-02 -3.4044266E-03 gauss-seidel spectral radius is 0.9986236 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 13:46:12 rms-change max change #iterations 3.947088 175.6608 at 10iterations 1.840340 63.13676 at 20iterations 0.8617516 30.94761 at 30iterations 0.4028076 13.85971 at 40iterations 0.1882119 6.360161 at 50iterations 8.8152125E-02 3.242966 at 60iterations 4.1147131E-02 1.322786 at 70iterations 1.9278158E-02 0.6499067 at 80iterations 8.9749666E-03 0.3115931 at 90iterations 4.2205262E-03 0.1751022 at 100iterations 1.9749608E-03 7.0306778E-02 at 110iterations 9.2963467E-04 3.5114288E-02 at 120iterations finished qdiffx linear iterations at : 13:46:21 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 9.2963467E-04 3.5114288E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 13:46:21 9.025u 0.277s 0:09.58 96.9% 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 15 2011 at 13:46:21 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 = 2279 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.872409 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): -18.42200 27.26100 ymin,ymax (A): -26.86400 28.90800 zmin,zma (A): -0.7110000 48.05900 x,y,z range (A): 45.68300 55.77200 48.77000 scale (grids/A): 2.872409 object centre (A): 4.419499 1.022000 23.67400 number of atom coordinates read : 2279 total number of charged atoms : 2200 net assigned charge : -2.999997 assigned positive charge : 334.1343 centred at (gu) : 88.19775 91.24153 82.08127 assigned negative charge : -337.1349 centred at (gu) : 87.97195 91.11243 81.74625 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 158045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20742 grid for indexing accessible points = 1.400000 m= 77753 mr = 113870 m= 28300 mr = 62648 m= 7010 mr = 22184 m= 1161 mr = 5181 m= 83 mr = 785 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 3013 time to turn everything in is 0.9400000 number of dielectric boundary points 67647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 17595 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) : 1.914939 object centre at (A) : 4.419499 1.022000 23.67400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3170081 0.1541182 midg,1,midg; midg,igrid,midg -3.2042939E-02 0.3551244 1,midg,midg; igrid,midg,midg -0.3041859 -3.8211025E-02 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 1.240000 now iterating at: 13:46:23 rms-change max change #iterations 9.295829 469.2572 at 10iterations 5.438477 123.9303 at 20iterations 3.170955 66.10410 at 30iterations 1.839312 48.21776 at 40iterations 1.065301 24.29419 at 50iterations 0.6154343 11.34450 at 60iterations 0.3550298 6.855652 at 70iterations 0.2049528 3.689493 at 80iterations 0.1179716 2.147965 at 90iterations 6.7874692E-02 1.216618 at 100iterations 3.8990993E-02 0.7343724 at 110iterations 2.2482872E-02 0.4151850 at 120iterations 1.2894833E-02 0.2542305 at 130iterations 7.3955259E-03 0.1401138 at 140iterations 4.2570080E-03 8.3835602E-02 at 150iterations 2.4437071E-03 4.9469739E-02 at 160iterations 1.4093171E-03 2.6636124E-02 at 170iterations 8.1295188E-04 1.5855789E-02 at 180iterations finished qdiffx linear iterations at : 13:46:41 total time elapsed so far: 14.79000 # loops : 180 mean,max change (kT/e) : 8.1295188E-04 1.5855789E-02 energy calculations done at 14.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.92000 DelPhi exited at 13:46:42 14.919u 0.317s 0:21.40 71.1% 0+0k 0+0io 0pf+0w