Tue Oct 11 08:05:16 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 Tue Oct 11 2011 at 08:05:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 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: 0.5016063 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 0.5016063 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 506.2292 centred at (gu) : 89.85197 91.06152 88.96694 assigned negative charge : -492.2308 centred at (gu) : 89.97559 91.14717 88.91218 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5580 nv = 96 ne = 84 npr = 64150 no. pairs analyzed = 64150 no. exposed pairs = 4842 no. arc points = 34743 no. surface atoms = 1619 nbur = 1777 mkacc time = 0.1400000 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 = 1.708000 m= 167 mr = 2449 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3359 ## 558 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7444 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6991137E-11 1.5188589E-10 midg,1,midg; midg,igrid,midg 1.7818882E-10 3.6838102E-11 1,midg,midg; igrid,midg,midg 2.9156449E-10 -1.6976380E-11 gauss-seidel spectral radius is 0.9795995 estimated iterations to convergence 58 setup time was (sec) 0.5400000 now iterating at: 08:05:17 rms-change max change #iterations 4.9468681E-02 9.262297 at 10iterations 2.5105628E-03 0.4386301 at 20iterations 1.4298111E-04 2.4122238E-02 at 30iterations 1.0997588E-05 1.3828278E-03 at 40iterations 1.2969329E-06 1.1634827E-04 at 50iterations finished qdiffx linear iterations at : 08:05:19 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.2969329E-06 1.1634827E-04 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 08:05:20 3.148u 0.151s 0:03.59 91.6% 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 Tue Oct 11 2011 at 08:05:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.504819 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 1.504819 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 506.2292 centred at (gu) : 89.55518 93.18331 86.90012 assigned negative charge : -492.2308 centred at (gu) : 89.92630 93.44104 86.73617 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15932 mr = 37684 m= 1184 mr = 9798 m= 15 mr = 400 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.4700000 number of dielectric boundary points 30814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 530 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 24244 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) : 0.5016063 object centre at (A) : 42.28450 27.93700 17.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9181325E-03 4.7110147E-03 midg,1,midg; midg,igrid,midg 1.4665356E-02 -7.7791614E-03 1,midg,midg; igrid,midg,midg 1.5482470E-02 -6.1130995E-04 gauss-seidel spectral radius is 0.9979087 estimated iterations to convergence 174 setup time was (sec) 0.7300000 now iterating at: 08:05:21 rms-change max change #iterations 2.905902 151.0665 at 10iterations 1.135229 49.35662 at 20iterations 0.4402878 17.96642 at 30iterations 0.1712103 6.383044 at 40iterations 6.7040361E-02 2.654998 at 50iterations 2.6071185E-02 0.9716225 at 60iterations 1.0144134E-02 0.3816584 at 70iterations 3.9575710E-03 0.1591954 at 80iterations 1.5449834E-03 5.8946609E-02 at 90iterations 6.0296984E-04 2.9781342E-02 at 100iterations 2.3526364E-04 9.8152161E-03 at 110iterations 9.1933609E-05 3.7364960E-03 at 120iterations finished qdiffx linear iterations at : 08:05:27 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 9.1933609E-05 3.7364960E-03 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 08:05:27 6.889u 0.168s 0:07.45 94.4% 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 08:05:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.257228 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 2.257228 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 506.2292 centred at (gu) : 89.33244 94.77471 85.34985 assigned negative charge : -492.2308 centred at (gu) : 89.88924 95.16127 85.10432 start vw surface at 0.2200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 143153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 57744 mr = 93902 m= 13451 mr = 42601 m= 1528 mr = 9138 m= 69 mr = 834 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 576 time to turn everything in is 1.070000 number of dielectric boundary points 69465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 25911 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) : 1.504819 object centre at (A) : 42.28450 27.93700 17.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1485282 6.9243103E-02 midg,1,midg; midg,igrid,midg 0.2305829 -0.1814305 1,midg,midg; igrid,midg,midg 0.2799604 -3.7249956E-02 gauss-seidel spectral radius is 0.9990668 estimated iterations to convergence 259 setup time was (sec) 1.350000 now iterating at: 08:05:29 rms-change max change #iterations 8.124161 250.8454 at 10iterations 4.521468 128.4326 at 20iterations 2.493344 65.36749 at 30iterations 1.359344 33.56713 at 40iterations 0.7386435 18.44403 at 50iterations 0.4003102 9.369560 at 60iterations 0.2163006 5.034815 at 70iterations 0.1166094 3.030334 at 80iterations 6.2846288E-02 1.586545 at 90iterations 3.3824507E-02 0.8220520 at 100iterations 1.8189920E-02 0.4473143 at 110iterations 9.7481851E-03 0.2145820 at 120iterations 5.2303551E-03 0.1094894 at 130iterations 2.8036570E-03 6.1014175E-02 at 140iterations 1.5047126E-03 3.3940077E-02 at 150iterations 8.0495962E-04 1.8306732E-02 at 160iterations 4.3165422E-04 8.8510513E-03 at 170iterations 2.3141153E-04 5.2738190E-03 at 180iterations finished qdiffx linear iterations at : 08:05:38 total time elapsed so far: 10.77000 # loops : 180 mean,max change (kT/e) : 2.3141153E-04 5.2738190E-03 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 08:05:39 10.946u 0.173s 0:11.45 97.0% 0+0k 0+0io 0pf+0w