Tue Oct 11 06:43:49 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 06:43:50 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7076972 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 0.7076972 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.04848 90.57604 90.47277 assigned negative charge : -303.8762 centred at (gu) : 90.23737 90.55816 90.50555 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6927 nv = 96 ne = 84 npr = 39943 no. pairs analyzed = 39943 no. exposed pairs = 2469 no. arc points = 16927 no. surface atoms = 841 nbur = 1358 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 431 mr = 3953 m= 4 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1621 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8399444E-08 4.6985335E-08 midg,1,midg; midg,igrid,midg 4.5231292E-08 7.5470403E-08 1,midg,midg; igrid,midg,midg 1.4737948E-07 -3.4601925E-08 gauss-seidel spectral radius is 0.9895875 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:43:50 rms-change max change #iterations 0.1994474 30.05588 at 10iterations 2.5245637E-02 3.380440 at 20iterations 3.3040026E-03 0.4535446 at 30iterations 5.2799738E-04 6.9026947E-02 at 40iterations 1.2137913E-04 1.6078949E-02 at 50iterations finished qdiffx linear iterations at : 06:43:54 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.2137913E-04 1.6078949E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 06:43:55 4.379u 0.382s 0:05.28 89.9% 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 06:43:55 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.123091 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 2.123091 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.14574 91.72791 91.41821 assigned negative charge : -303.8762 centred at (gu) : 90.71218 91.67459 91.51682 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16927 grid for indexing accessible points = 1.400000 m= 29346 mr = 52733 m= 5630 mr = 22244 m= 562 mr = 3784 m= 10 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15143 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) : 0.7076972 object centre at (A) : 24.98300 20.57300 21.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9777748E-02 6.5756232E-02 midg,1,midg; midg,igrid,midg 4.1410625E-03 3.2292876E-02 1,midg,midg; igrid,midg,midg 4.3416828E-02 9.4846254E-03 gauss-seidel spectral radius is 0.9988281 estimated iterations to convergence 231 setup time was (sec) 0.9100000 now iterating at: 06:43:56 rms-change max change #iterations 4.582754 195.1512 at 10iterations 2.267195 74.36247 at 20iterations 1.124850 35.27585 at 30iterations 0.5576376 17.63195 at 40iterations 0.2777070 8.240997 at 50iterations 0.1376584 4.280283 at 60iterations 6.8363219E-02 2.008900 at 70iterations 3.4139205E-02 1.100544 at 80iterations 1.7061515E-02 0.5209080 at 90iterations 8.5991668E-03 0.2568226 at 100iterations 4.3257475E-03 0.1287079 at 110iterations 2.2315045E-03 6.6460609E-02 at 120iterations finished qdiffx linear iterations at : 06:44:06 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 2.2315045E-03 6.6460609E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.46000 DelPhi exited at 06:44:06 10.464u 0.445s 0:11.23 97.0% 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 06:44:06 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.184637 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 3.184637 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.21858 92.59184 92.12745 assigned negative charge : -303.8762 centred at (gu) : 91.06818 92.51184 92.27520 start vw surface at 0.1000000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 170699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16927 grid for indexing accessible points = 1.400000 m= 92173 mr = 126968 m= 36799 mr = 76659 m= 10788 mr = 30289 m= 2255 mr = 8333 m= 269 mr = 1667 m= 11 mr = 159 m= 0 mr = 5 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 68914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15383 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) : 2.123091 object centre at (A) : 24.98300 20.57300 21.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3272117 0.6957539 midg,1,midg; midg,igrid,midg -3.3798891E-03 0.2461625 1,midg,midg; igrid,midg,midg 0.3306714 0.2177510 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.210000 now iterating at: 06:44:09 rms-change max change #iterations 10.15913 320.0394 at 10iterations 5.999356 175.8870 at 20iterations 3.537757 75.99116 at 30iterations 2.084855 43.06943 at 40iterations 1.226220 25.25882 at 50iterations 0.7202100 13.65646 at 60iterations 0.4224808 8.230915 at 70iterations 0.2477669 4.572987 at 80iterations 0.1448837 2.688662 at 90iterations 8.4922314E-02 1.443281 at 100iterations 4.9855676E-02 0.9159431 at 110iterations 2.9363375E-02 0.5063553 at 120iterations 1.7368959E-02 0.3180351 at 130iterations 1.0398999E-02 0.2026596 at 140iterations 6.3685062E-03 0.1160431 at 150iterations 4.0220972E-03 8.3312988E-02 at 160iterations 2.6673789E-03 5.5198669E-02 at 170iterations 1.8670907E-03 3.9363861E-02 at 180iterations finished qdiffx linear iterations at : 06:44:25 total time elapsed so far: 18.16000 # loops : 180 mean,max change (kT/e) : 1.8670907E-03 3.9363861E-02 energy calculations done at 18.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.32000 DelPhi exited at 06:44:25 18.327u 0.475s 0:19.27 97.5% 0+0k 0+0io 0pf+0w