Mon Oct 10 17:04:29 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 Mon Oct 10 2011 at 17:04:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6564995 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 0.6564995 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.999985 assigned positive charge : 281.3191 centred at (gu) : 90.10803 89.24984 87.88402 assigned negative charge : -288.3190 centred at (gu) : 90.38490 89.45815 88.27177 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5741 nv = 96 ne = 84 npr = 40409 no. pairs analyzed = 40409 no. exposed pairs = 2703 no. arc points = 19754 no. surface atoms = 907 nbur = 1061 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 277 mr = 2762 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2400000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1884 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1928108E-08 -4.5958529E-08 midg,1,midg; midg,igrid,midg 1.1859423E-08 -3.9194113E-08 1,midg,midg; igrid,midg,midg 1.8230152E-08 -5.6768783E-08 gauss-seidel spectral radius is 0.9879292 estimated iterations to convergence 74 setup time was (sec) 0.4700000 now iterating at: 17:04:29 rms-change max change #iterations 0.1446337 27.81551 at 10iterations 1.5102878E-02 2.465254 at 20iterations 1.5207910E-03 0.2557697 at 30iterations 1.5679775E-04 2.3222923E-02 at 40iterations 1.6469789E-05 2.8114319E-03 at 50iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.6469789E-05 2.8114319E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 17:04:34 3.307u 0.202s 0:04.93 70.9% 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 Mon Oct 10 2011 at 17:04:34 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.969499 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 1.969499 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.999985 assigned positive charge : 281.3191 centred at (gu) : 90.32429 87.74963 83.65222 assigned negative charge : -288.3190 centred at (gu) : 91.15472 88.37450 84.81514 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 19292 mr = 39438 m= 2648 mr = 13143 m= 154 mr = 1413 m= 6 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.4700000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14516 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) : 0.6564995 object centre at (A) : 50.73100 30.60000 15.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4137072E-02 -4.2257324E-02 midg,1,midg; midg,igrid,midg 2.9514138E-02 -1.7687215E-02 1,midg,midg; igrid,midg,midg -2.4442749E-02 -5.1420808E-02 gauss-seidel spectral radius is 0.9986644 estimated iterations to convergence 217 setup time was (sec) 0.7800000 now iterating at: 17:04:35 rms-change max change #iterations 3.799736 169.5410 at 10iterations 1.785082 65.19443 at 20iterations 0.8340702 28.41972 at 30iterations 0.3927793 13.13825 at 40iterations 0.1847716 6.694687 at 50iterations 8.7198511E-02 3.086670 at 60iterations 4.0982600E-02 1.479385 at 70iterations 1.9237787E-02 0.6836853 at 80iterations 9.1033224E-03 0.3228951 at 90iterations 4.2725019E-03 0.1371746 at 100iterations 2.0089357E-03 7.2271347E-02 at 110iterations 9.4604451E-04 3.2788277E-02 at 120iterations finished qdiffx linear iterations at : 17:04:42 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 9.4604451E-04 3.2788277E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 17:04:43 8.741u 0.210s 0:09.88 90.5% 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 17:04:44 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.954248 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 2.954248 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.999985 assigned positive charge : 281.3191 centred at (gu) : 90.48643 86.62437 80.47835 assigned negative charge : -288.3190 centred at (gu) : 91.73208 87.56171 82.22269 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 142496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 64195 mr = 96235 m= 20927 mr = 50059 m= 4463 mr = 15862 m= 643 mr = 3051 m= 42 mr = 415 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.6399999 no. cavity mid-points inaccessible to solvent = 1996 time to turn everything in is 1.200000 number of dielectric boundary points 67123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 14688 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) : 1.969499 object centre at (A) : 50.73100 30.60000 15.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5954893 -0.3535852 midg,1,midg; midg,igrid,midg 0.3044551 -0.1671244 1,midg,midg; igrid,midg,midg -0.3672608 -0.5037783 gauss-seidel spectral radius is 0.9992697 estimated iterations to convergence 292 setup time was (sec) 1.520000 now iterating at: 17:04:46 rms-change max change #iterations 8.866421 382.4014 at 10iterations 5.181222 130.9358 at 20iterations 3.020301 72.91174 at 30iterations 1.746003 40.67862 at 40iterations 1.010845 23.80970 at 50iterations 0.5816664 13.65038 at 60iterations 0.3367043 6.535324 at 70iterations 0.1935376 3.746559 at 80iterations 0.1113824 2.369021 at 90iterations 6.4103372E-02 1.303871 at 100iterations 3.6837798E-02 0.7253494 at 110iterations 2.1171885E-02 0.4031982 at 120iterations 1.2193177E-02 0.2310715 at 130iterations 7.0103165E-03 0.1427498 at 140iterations 4.0408554E-03 8.6797714E-02 at 150iterations 2.3170453E-03 4.6353608E-02 at 160iterations 1.3359217E-03 2.5165558E-02 at 170iterations 7.6877238E-04 1.5399933E-02 at 180iterations finished qdiffx linear iterations at : 17:04:57 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 7.6877238E-04 1.5399933E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 17:04:58 12.609u 0.217s 0:13.42 95.4% 0+0k 0+0io 0pf+0w