Tue Oct 11 03:40:23 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 Tue Oct 11 2011 at 03:40:23 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6067837 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 0.6067837 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2681 net assigned charge : -0.2989812 assigned positive charge : 433.9147 centred at (gu) : 90.24551 90.54314 92.31907 assigned negative charge : -434.2142 centred at (gu) : 89.99366 90.40362 92.19214 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 58399 no. pairs analyzed = 58399 no. exposed pairs = 3350 no. arc points = 23128 no. surface atoms = 1134 nbur = 1704 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3803 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 3251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2394 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8527 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0358237E-09 1.0079614E-08 midg,1,midg; midg,igrid,midg -6.5902750E-09 7.3529169E-09 1,midg,midg; igrid,midg,midg -1.2603167E-08 1.2544895E-08 gauss-seidel spectral radius is 0.9859533 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 03:40:24 rms-change max change #iterations 0.1248341 19.77280 at 10iterations 1.1113717E-02 1.816780 at 20iterations 1.0063304E-03 0.1532183 at 30iterations 1.1453140E-04 1.5692234E-02 at 40iterations 2.2614384E-05 3.7732124E-03 at 50iterations finished qdiffx linear iterations at : 03:40:26 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 2.2614384E-05 3.7732124E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 03:40:27 3.169u 0.161s 0:03.80 87.3% 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 Tue Oct 11 2011 at 03:40:27 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.820351 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 1.820351 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2681 net assigned charge : -0.2989812 assigned positive charge : 433.9147 centred at (gu) : 90.73620 91.62888 96.95676 assigned negative charge : -434.2142 centred at (gu) : 89.98063 91.21067 96.57623 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23128 grid for indexing accessible points = 1.400000 m= 26108 mr = 51953 m= 3421 mr = 19387 m= 155 mr = 2092 m= 0 mr = 50 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.5100000 number of dielectric boundary points 29961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20979 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) : 0.6067837 object centre at (A) : 12.33000 -2.731000 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2840670E-02 3.0024941E-03 midg,1,midg; midg,igrid,midg -1.1249447E-02 1.1696399E-02 1,midg,midg; igrid,midg,midg -9.2829373E-03 4.2935800E-02 gauss-seidel spectral radius is 0.9985257 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 03:40:28 rms-change max change #iterations 4.166296 184.0527 at 10iterations 1.895420 73.54427 at 20iterations 0.8627887 32.92869 at 30iterations 0.3929569 12.80807 at 40iterations 0.1795845 5.947777 at 50iterations 8.1903778E-02 3.111910 at 60iterations 3.7267294E-02 1.184319 at 70iterations 1.6996462E-02 0.5556564 at 80iterations 7.7452660E-03 0.2446289 at 90iterations 3.5229789E-03 0.1160698 at 100iterations 1.6094242E-03 5.4726601E-02 at 110iterations 7.3691196E-04 2.2410870E-02 at 120iterations finished qdiffx linear iterations at : 03:40:34 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 7.3691196E-04 2.2410870E-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) 7.030000 DelPhi exited at 03:40:35 7.032u 0.201s 0:07.86 91.9% 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 Tue Oct 11 2011 at 03:40:35 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.730527 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 2.730527 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2681 net assigned charge : -0.2989812 assigned positive charge : 433.9147 centred at (gu) : 91.10417 92.44337 100.4351 assigned negative charge : -434.2142 centred at (gu) : 89.97090 91.81592 99.86443 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 170925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23128 grid for indexing accessible points = 1.400000 m= 86605 mr = 125809 m= 28576 mr = 71375 m= 5957 mr = 23019 m= 714 mr = 4560 m= 37 mr = 468 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 3894 time to turn everything in is 1.270000 number of dielectric boundary points 67576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 21444 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) : 1.820351 object centre at (A) : 12.33000 -2.731000 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.348604 0.2349751 midg,1,midg; midg,igrid,midg -0.1408814 0.1538320 1,midg,midg; igrid,midg,midg -6.2024336E-02 0.4272811 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.550000 now iterating at: 03:40:37 rms-change max change #iterations 9.850270 299.9922 at 10iterations 5.663384 118.4505 at 20iterations 3.240856 75.72945 at 30iterations 1.847618 38.55624 at 40iterations 1.052732 20.25855 at 50iterations 0.6003310 11.05786 at 60iterations 0.3416107 6.050756 at 70iterations 0.1946474 3.584850 at 80iterations 0.1102820 2.094608 at 90iterations 6.2708415E-02 1.175502 at 100iterations 3.5669155E-02 0.6665611 at 110iterations 2.0273712E-02 0.3836098 at 120iterations 1.1507195E-02 0.2190962 at 130iterations 6.5596849E-03 0.1293879 at 140iterations 3.7105831E-03 6.5668106E-02 at 150iterations 2.1072731E-03 3.9466858E-02 at 160iterations 1.1984534E-03 2.1757126E-02 at 170iterations 6.8004348E-04 1.2697220E-02 at 180iterations finished qdiffx linear iterations at : 03:40:46 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 6.8004348E-04 1.2697220E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.47000 DelPhi exited at 03:40:47 11.468u 0.223s 0:12.02 97.1% 0+0k 0+0io 0pf+0w