Tue Oct 11 07:07:56 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 07:07:56 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3756 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: SEP 191 has a net charge of -0.4750 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5496542 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): -10.43900 54.32900 ymin,ymax (A): -35.09300 22.51800 zmin,zma (A): 67.88700 118.4120 x,y,z range (A): 64.76800 57.61100 50.52500 scale (grids/A): 0.5496542 object centre (A): 21.94500 -6.287501 93.14951 number of atom coordinates read : 3756 total number of charged atoms : 3608 net assigned charge : 7.945033 assigned positive charge : 572.2563 centred at (gu) : 90.17941 89.06895 90.42421 assigned negative charge : -564.3137 centred at (gu) : 90.15261 88.90973 90.44603 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7202 nv = 96 ne = 84 npr = 76665 no. pairs analyzed = 76665 no. exposed pairs = 4557 no. arc points = 31025 no. surface atoms = 1526 nbur = 2230 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 298 mr = 3961 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3130 ## 384 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2070644E-10 4.1599410E-10 midg,1,midg; midg,igrid,midg -1.2486482E-09 1.6677144E-09 1,midg,midg; igrid,midg,midg 3.1520977E-10 8.8381652E-10 gauss-seidel spectral radius is 0.9829847 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 07:07:57 rms-change max change #iterations 8.6529583E-02 13.46493 at 10iterations 6.5986896E-03 0.9871311 at 20iterations 1.1281815E-03 0.2087212 at 30iterations 4.0927270E-04 7.8677177E-02 at 40iterations 1.5654170E-04 3.0332565E-02 at 50iterations finished qdiffx linear iterations at : 07:07:59 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.5654170E-04 3.0332565E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 07:08:00 3.157u 0.148s 0:03.88 84.7% 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 Tue Oct 11 2011 at 07:08:00 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3756 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: SEP 191 has a net charge of -0.4750 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.648962 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): -10.43900 54.32900 ymin,ymax (A): -35.09300 22.51800 zmin,zma (A): 67.88700 118.4120 x,y,z range (A): 64.76800 57.61100 50.52500 scale (grids/A): 1.648962 object centre (A): 21.94500 -6.287501 93.14951 number of atom coordinates read : 3756 total number of charged atoms : 3608 net assigned charge : 7.945033 assigned positive charge : 572.2563 centred at (gu) : 90.53719 87.20531 91.27152 assigned negative charge : -564.3137 centred at (gu) : 90.45748 86.72878 91.33763 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25999 mr = 56187 m= 2696 mr = 18699 m= 55 mr = 1394 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1184 time to turn everything in is 0.5800000 number of dielectric boundary points 32625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 346 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 27656 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) : 0.5496542 object centre at (A) : 21.94500 -6.287501 93.14951 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1853884E-03 -1.5238697E-03 midg,1,midg; midg,igrid,midg -1.5135650E-02 1.6561935E-02 1,midg,midg; igrid,midg,midg 1.7796898E-02 1.7843785E-02 gauss-seidel spectral radius is 0.9982961 estimated iterations to convergence 192 setup time was (sec) 0.8300000 now iterating at: 07:08:01 rms-change max change #iterations 3.935082 163.3580 at 10iterations 1.686346 59.14089 at 20iterations 0.7263550 23.16871 at 30iterations 0.3107762 9.529251 at 40iterations 0.1344261 3.847399 at 50iterations 5.7542168E-02 1.765308 at 60iterations 2.4709651E-02 0.7704043 at 70iterations 1.0706714E-02 0.3376160 at 80iterations 4.6596131E-03 0.1406040 at 90iterations 2.0764000E-03 6.9160461E-02 at 100iterations 9.7146071E-04 3.6827087E-02 at 110iterations 5.0161441E-04 1.8955231E-02 at 120iterations finished qdiffx linear iterations at : 07:08:07 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 5.0161441E-04 1.8955231E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 07:08:08 6.885u 0.172s 0:07.50 94.0% 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 07:08:08 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3756 !!! WARNING: GLM 189 has a net charge of -0.0940 !!! WARNING: SEP 191 has a net charge of -0.4750 !!! WARNING: HIR 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.473444 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): -10.43900 54.32900 ymin,ymax (A): -35.09300 22.51800 zmin,zma (A): 67.88700 118.4120 x,y,z range (A): 64.76800 57.61100 50.52500 scale (grids/A): 2.473444 object centre (A): 21.94500 -6.287501 93.14951 number of atom coordinates read : 3756 total number of charged atoms : 3608 net assigned charge : 7.945033 assigned positive charge : 572.2563 centred at (gu) : 90.80556 85.80769 91.90681 assigned negative charge : -564.3137 centred at (gu) : 90.68611 85.09306 92.00622 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 186388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88720 mr = 136859 m= 26673 mr = 71731 m= 4262 mr = 20945 m= 207 mr = 2915 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 4065 time to turn everything in is 1.310000 number of dielectric boundary points 73745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 28830 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) : 1.648962 object centre at (A) : 21.94500 -6.287501 93.14951 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9064518E-02 -6.1564058E-02 midg,1,midg; midg,igrid,midg -0.1697575 0.1866641 1,midg,midg; igrid,midg,midg 0.3075647 -0.1226942 gauss-seidel spectral radius is 0.9991863 estimated iterations to convergence 277 setup time was (sec) 1.590000 now iterating at: 07:08:10 rms-change max change #iterations 9.937349 317.8256 at 10iterations 5.647390 161.7260 at 20iterations 3.200500 75.58125 at 30iterations 1.804328 47.51763 at 40iterations 1.016402 23.02074 at 50iterations 0.5708604 11.18334 at 60iterations 0.3209590 6.276545 at 70iterations 0.1800410 3.381447 at 80iterations 0.1009086 1.856873 at 90iterations 5.6474946E-02 1.186520 at 100iterations 3.1663418E-02 0.5786781 at 110iterations 1.7757941E-02 0.3112259 at 120iterations 9.9428026E-03 0.1933641 at 130iterations 5.6038843E-03 0.1127801 at 140iterations 3.1670625E-03 6.2019348E-02 at 150iterations 1.8120873E-03 3.6655426E-02 at 160iterations 1.0631813E-03 2.1885872E-02 at 170iterations 6.4676767E-04 1.5823364E-02 at 180iterations finished qdiffx linear iterations at : 07:08:19 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 6.4676767E-04 1.5823364E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 07:08:20 11.091u 0.167s 0:11.66 96.4% 0+0k 0+0io 0pf+0w