Sat Oct 8 14:50:10 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 14:50:10 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 = 2968 !!! 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: 0.6368629 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 0.6368629 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.228008 assigned positive charge : 443.8537 centred at (gu) : 88.79524 90.05080 91.51165 assigned negative charge : -442.6264 centred at (gu) : 88.71967 89.90403 91.50473 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8001 nv = 96 ne = 84 npr = 62061 no. pairs analyzed = 62061 no. exposed pairs = 3365 no. arc points = 23723 no. surface atoms = 1149 nbur = 1819 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4659 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2340 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7062983E-10 3.5715322E-09 midg,1,midg; midg,igrid,midg -1.6210265E-08 1.9522455E-08 1,midg,midg; igrid,midg,midg -9.8474118E-09 8.3726199E-09 gauss-seidel spectral radius is 0.9872555 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 14:50:11 rms-change max change #iterations 0.1514538 19.78216 at 10iterations 1.5177755E-02 2.182777 at 20iterations 1.5785808E-03 0.2157288 at 30iterations 1.7712120E-04 2.4201870E-02 at 40iterations 2.6029033E-05 4.0035248E-03 at 50iterations finished qdiffx linear iterations at : 14:50:14 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.6029033E-05 4.0035248E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 14:50:15 4.121u 0.295s 0:04.73 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 8 2011 at 14:50:15 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 = 2968 !!! 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: 1.910589 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 1.910589 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.228008 assigned positive charge : 443.8537 centred at (gu) : 86.38521 90.15214 94.53409 assigned negative charge : -442.6264 centred at (gu) : 86.15891 89.71191 94.51369 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23723 grid for indexing accessible points = 1.400000 m= 31268 mr = 62879 m= 4496 mr = 23349 m= 282 mr = 2733 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 34262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22189 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) : 0.6368629 object centre at (A) : 15.56000 -0.8410006 20.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5172470E-03 9.0292674E-03 midg,1,midg; midg,igrid,midg 6.4363121E-04 2.7883692E-02 1,midg,midg; igrid,midg,midg -3.7745140E-02 2.4018323E-02 gauss-seidel spectral radius is 0.9986730 estimated iterations to convergence 217 setup time was (sec) 1.070000 now iterating at: 14:50:16 rms-change max change #iterations 4.632672 222.6965 at 10iterations 2.197401 69.64223 at 20iterations 1.044707 32.67958 at 30iterations 0.4944742 14.57329 at 40iterations 0.2343740 6.535683 at 50iterations 0.1110909 3.325737 at 60iterations 5.2535091E-02 1.434759 at 70iterations 2.4877338E-02 0.7624488 at 80iterations 1.1816200E-02 0.3617821 at 90iterations 5.6184763E-03 0.1677427 at 100iterations 2.6661290E-03 8.1808090E-02 at 110iterations 1.2696126E-03 3.9514542E-02 at 120iterations finished qdiffx linear iterations at : 14:50:25 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 1.2696126E-03 3.9514542E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 14:50:25 9.677u 0.294s 0:10.29 96.7% 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 14:50:25 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 = 2968 !!! 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: 2.865883 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 2.865883 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.228008 assigned positive charge : 443.8537 centred at (gu) : 84.57769 90.22803 96.80083 assigned negative charge : -442.6264 centred at (gu) : 84.23834 89.56778 96.77048 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 201921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23723 grid for indexing accessible points = 1.400000 m= 102593 mr = 151499 m= 35552 mr = 85290 m= 8073 mr = 28555 m= 1204 mr = 6010 m= 74 mr = 820 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 77219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 22584 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) : 1.910589 object centre at (A) : 15.56000 -0.8410006 20.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7699614E-02 0.2248850 midg,1,midg; midg,igrid,midg 1.6825294E-02 0.2958047 1,midg,midg; igrid,midg,midg -0.2866937 0.3291435 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.280000 now iterating at: 14:50:28 rms-change max change #iterations 10.70250 480.1407 at 10iterations 6.257741 122.1621 at 20iterations 3.629560 71.90935 at 30iterations 2.108072 47.52341 at 40iterations 1.219838 22.58994 at 50iterations 0.7069637 12.92118 at 60iterations 0.4094422 7.092492 at 70iterations 0.2371252 3.991997 at 80iterations 0.1371266 2.251616 at 90iterations 7.9116672E-02 1.382992 at 100iterations 4.5648914E-02 0.8017159 at 110iterations 2.6421502E-02 0.4894562 at 120iterations 1.5267908E-02 0.2655816 at 130iterations 8.8142483E-03 0.1490746 at 140iterations 5.1003625E-03 8.4011078E-02 at 150iterations 2.9507158E-03 4.7536850E-02 at 160iterations 1.7152658E-03 2.8194666E-02 at 170iterations 9.9555706E-04 1.6769409E-02 at 180iterations finished qdiffx linear iterations at : 14:50:42 total time elapsed so far: 16.19000 # loops : 180 mean,max change (kT/e) : 9.9555706E-04 1.6769409E-02 energy calculations done at 16.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.37000 DelPhi exited at 14:50:42 16.367u 0.328s 0:17.02 98.0% 0+0k 0+0io 0pf+0w