Sat Oct 8 18:35:57 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 18:35:57 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6194105 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): -32.25000 17.39000 ymin,ymax (A): -23.10700 22.73500 zmin,zma (A): -12.64200 44.83200 x,y,z range (A): 49.64000 45.84200 57.47400 scale (grids/A): 0.6194105 object centre (A): -7.430000 -0.1860008 16.09500 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 88.64114 89.17441 89.87170 assigned negative charge : -386.9045 centred at (gu) : 88.54945 89.22609 89.73020 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6451 nv = 96 ne = 84 npr = 54456 no. pairs analyzed = 54456 no. exposed pairs = 2935 no. arc points = 20647 no. surface atoms = 993 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3663 m= 0 mr = 54 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 164 time to turn everything in is 0.2900000 number of dielectric boundary points 3061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8799596E-09 1.2326542E-08 midg,1,midg; midg,igrid,midg 8.3590379E-09 2.4165683E-10 1,midg,midg; igrid,midg,midg -3.3258507E-09 7.0815007E-09 gauss-seidel spectral radius is 0.9864957 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 18:35:58 rms-change max change #iterations 0.1247575 21.12329 at 10iterations 1.1539262E-02 1.685740 at 20iterations 1.0468151E-03 0.1668053 at 30iterations 9.7553580E-05 1.4987946E-02 at 40iterations 8.9586902E-06 1.4209747E-03 at 50iterations finished qdiffx linear iterations at : 18:36:00 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 8.9586902E-06 1.4209747E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 18:36:01 3.335u 0.193s 0:03.80 92.6% 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 18:36:01 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.858232 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): -32.25000 17.39000 ymin,ymax (A): -23.10700 22.73500 zmin,zma (A): -12.64200 44.83200 x,y,z range (A): 49.64000 45.84200 57.47400 scale (grids/A): 1.858232 object centre (A): -7.430000 -0.1860008 16.09500 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 85.92334 87.52264 89.61459 assigned negative charge : -386.9045 centred at (gu) : 85.64816 87.67793 89.19051 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20647 grid for indexing accessible points = 1.400000 m= 24866 mr = 49838 m= 3622 mr = 18660 m= 193 mr = 2318 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4959 time to turn everything in is 0.5100000 number of dielectric boundary points 28218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19228 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) : 0.6194105 object centre at (A) : -7.430000 -0.1860008 16.09500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1908199E-02 3.5040066E-02 midg,1,midg; midg,igrid,midg 1.2731020E-02 2.9534630E-03 1,midg,midg; igrid,midg,midg -4.4078878E-03 3.3750832E-02 gauss-seidel spectral radius is 0.9985602 estimated iterations to convergence 209 setup time was (sec) 0.8000000 now iterating at: 18:36:02 rms-change max change #iterations 4.009709 170.3705 at 10iterations 1.838005 58.51939 at 20iterations 0.8415633 27.67846 at 30iterations 0.3864574 12.55431 at 40iterations 0.1781006 5.582624 at 50iterations 8.1436180E-02 2.927831 at 60iterations 3.7475966E-02 1.372676 at 70iterations 1.7196557E-02 0.5517373 at 80iterations 7.9218857E-03 0.2568188 at 90iterations 3.6234637E-03 0.1143909 at 100iterations 1.6694587E-03 5.3695679E-02 at 110iterations 7.6573296E-04 2.4070740E-02 at 120iterations finished qdiffx linear iterations at : 18:36:08 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 7.6573296E-04 2.4070740E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 18:36:09 7.450u 0.207s 0:07.99 95.7% 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 18:36:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.787347 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): -32.25000 17.39000 ymin,ymax (A): -23.10700 22.73500 zmin,zma (A): -12.64200 44.83200 x,y,z range (A): 49.64000 45.84200 57.47400 scale (grids/A): 2.787347 object centre (A): -7.430000 -0.1860008 16.09500 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 83.88487 86.28380 89.42184 assigned negative charge : -386.9045 centred at (gu) : 83.47219 86.51687 88.78573 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20647 grid for indexing accessible points = 1.400000 m= 82096 mr = 120260 m= 28350 mr = 68296 m= 6465 mr = 23034 m= 898 mr = 5011 m= 62 mr = 643 m= 0 mr = 30 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 17564 time to turn everything in is 1.250000 number of dielectric boundary points 63642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19622 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) : 1.858232 object centre at (A) : -7.430000 -0.1860008 16.09500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1505493 0.5016618 midg,1,midg; midg,igrid,midg 0.1453614 3.3261284E-02 1,midg,midg; igrid,midg,midg -3.0395245E-02 0.4537496 gauss-seidel spectral radius is 0.9992309 estimated iterations to convergence 285 setup time was (sec) 1.560000 now iterating at: 18:36:11 rms-change max change #iterations 9.356468 374.9446 at 10iterations 5.318655 109.8819 at 20iterations 3.014996 56.34251 at 30iterations 1.714352 32.71036 at 40iterations 0.9682413 17.27261 at 50iterations 0.5491977 10.08405 at 60iterations 0.3114785 5.734642 at 70iterations 0.1765711 3.289423 at 80iterations 0.1001345 1.841160 at 90iterations 5.6797389E-02 1.010879 at 100iterations 3.2244626E-02 0.5960579 at 110iterations 1.8275416E-02 0.3761730 at 120iterations 1.0351925E-02 0.1807709 at 130iterations 5.8884430E-03 0.1066380 at 140iterations 3.3390035E-03 6.7794800E-02 at 150iterations 1.8917876E-03 3.4645677E-02 at 160iterations 1.0711801E-03 2.0488739E-02 at 170iterations 6.0968695E-04 1.0939598E-02 at 180iterations finished qdiffx linear iterations at : 18:36:21 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 6.0968695E-04 1.0939598E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 18:36:22 12.024u 0.219s 0:12.55 97.4% 0+0k 0+0io 0pf+0w