Mon Oct 10 14:13:41 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 Mon Oct 10 2011 at 14:13:42 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 61 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7043090 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 0.7043090 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2039 net assigned charge : -1.054990 assigned positive charge : 330.9267 centred at (gu) : 90.42755 89.64433 90.74680 assigned negative charge : -331.9820 centred at (gu) : 90.18784 89.76985 90.64709 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7394 nv = 96 ne = 84 npr = 44199 no. pairs analyzed = 44199 no. exposed pairs = 2699 no. arc points = 18903 no. surface atoms = 915 nbur = 1267 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4102 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1800000 number of dielectric boundary points 3685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1702 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8123 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0589261E-08 4.5610363E-08 midg,1,midg; midg,igrid,midg 5.5400470E-08 -6.6712644E-08 1,midg,midg; igrid,midg,midg -1.1910115E-07 1.1505411E-07 gauss-seidel spectral radius is 0.9895082 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 14:13:42 rms-change max change #iterations 0.2089068 33.01907 at 10iterations 2.5425313E-02 3.126734 at 20iterations 3.2672668E-03 0.4898586 at 30iterations 4.4278670E-04 5.7559967E-02 at 40iterations 7.3323412E-05 1.1264801E-02 at 50iterations finished qdiffx linear iterations at : 14:13:45 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.3323412E-05 1.1264801E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:13:45 3.332u 0.148s 0:03.89 89.2% 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 Mon Oct 10 2011 at 14:13:45 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 61 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.112927 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 2.112927 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2039 net assigned charge : -1.054990 assigned positive charge : 330.9267 centred at (gu) : 91.28251 88.93266 92.24050 assigned negative charge : -331.9820 centred at (gu) : 90.56354 89.30972 91.94118 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18903 grid for indexing accessible points = 1.400000 m= 31364 mr = 54634 m= 5934 mr = 23512 m= 492 mr = 3946 m= 10 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.3800000 number of dielectric boundary points 33875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16188 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) : 0.7043090 object centre at (A) : 11.31650 0.7330008 15.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2143570E-03 -6.4985058E-03 midg,1,midg; midg,igrid,midg 1.3354523E-02 -2.4937335E-02 1,midg,midg; igrid,midg,midg -2.5838131E-02 -1.7572248E-02 gauss-seidel spectral radius is 0.9988409 estimated iterations to convergence 232 setup time was (sec) 0.5900000 now iterating at: 14:13:46 rms-change max change #iterations 4.809496 228.7897 at 10iterations 2.364688 86.41410 at 20iterations 1.178298 39.06332 at 30iterations 0.5819985 16.92737 at 40iterations 0.2900429 8.638454 at 50iterations 0.1444715 3.925535 at 60iterations 7.1751162E-02 2.090412 at 70iterations 3.5622597E-02 1.101563 at 80iterations 1.7813902E-02 0.5273256 at 90iterations 8.9049237E-03 0.2570705 at 100iterations 4.4554975E-03 0.1488533 at 110iterations 2.2477095E-03 6.3822746E-02 at 120iterations finished qdiffx linear iterations at : 14:13:53 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 2.2477095E-03 6.3822746E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:13:54 7.648u 0.194s 0:08.53 91.7% 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 Mon Oct 10 2011 at 14:13:54 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 61 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.169390 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 3.169390 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2039 net assigned charge : -1.054990 assigned positive charge : 330.9267 centred at (gu) : 91.92380 88.39904 93.36069 assigned negative charge : -331.9820 centred at (gu) : 90.84521 88.96458 92.91180 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 180680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18903 grid for indexing accessible points = 1.400000 m= 97293 mr = 131683 m= 39978 mr = 80558 m= 11239 mr = 32662 m= 2031 mr = 8588 m= 172 mr = 1460 m= 9 mr = 78 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1331 time to turn everything in is 1.170000 number of dielectric boundary points 76373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16312 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) : 2.112927 object centre at (A) : 11.31650 0.7330008 15.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4369523E-02 -0.1392521 midg,1,midg; midg,igrid,midg 0.1155806 -0.2072818 1,midg,midg; igrid,midg,midg -0.1625134 -0.3148140 gauss-seidel spectral radius is 0.9993031 estimated iterations to convergence 299 setup time was (sec) 1.400000 now iterating at: 14:13:56 rms-change max change #iterations 10.75497 416.3515 at 10iterations 6.389800 155.3809 at 20iterations 3.803838 87.79849 at 30iterations 2.257985 49.36436 at 40iterations 1.333445 25.85773 at 50iterations 0.7857411 16.16332 at 60iterations 0.4641858 9.271258 at 70iterations 0.2722655 5.154536 at 80iterations 0.1600870 2.939384 at 90iterations 9.4163656E-02 1.645777 at 100iterations 5.5370480E-02 1.021616 at 110iterations 3.2584138E-02 0.6064835 at 120iterations 1.9266007E-02 0.3583565 at 130iterations 1.1485287E-02 0.1903658 at 140iterations 6.9075944E-03 0.1262207 at 150iterations 4.2272885E-03 8.4171295E-02 at 160iterations 2.6692830E-03 5.6255341E-02 at 170iterations 1.7537785E-03 3.6602020E-02 at 180iterations finished qdiffx linear iterations at : 14:14:07 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.7537785E-03 3.6602020E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 14:14:08 12.606u 0.216s 0:13.47 95.1% 0+0k 0+0io 0pf+0w