Sat Oct 15 13:05:13 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 15 2011 at 13:05:13 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 = 2656 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: 0.6368173 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 0.6368173 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2512 net assigned charge : 6.500010 assigned positive charge : 407.7894 centred at (gu) : 90.69038 90.37038 90.75574 assigned negative charge : -401.2902 centred at (gu) : 90.63959 90.23818 90.84366 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7218 nv = 96 ne = 84 npr = 52126 no. pairs analyzed = 52126 no. exposed pairs = 3390 no. arc points = 24093 no. surface atoms = 1143 nbur = 1513 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3820 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2000000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2459 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5531349E-08 -1.4955326E-09 midg,1,midg; midg,igrid,midg -5.6802514E-09 2.4923573E-08 1,midg,midg; igrid,midg,midg 2.6212750E-09 1.6448228E-08 gauss-seidel spectral radius is 0.9872332 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 13:05:14 rms-change max change #iterations 0.1431391 27.85640 at 10iterations 1.4147275E-02 1.853190 at 20iterations 1.4550849E-03 0.2110977 at 30iterations 1.8398586E-04 2.7328491E-02 at 40iterations 3.2421449E-05 4.8637390E-03 at 50iterations finished qdiffx linear iterations at : 13:05:17 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 3.2421449E-05 4.8637390E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 13:05:17 3.520u 0.193s 0:04.05 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 Sat Oct 15 2011 at 13:05:17 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 = 2656 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: 1.910452 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 1.910452 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2512 net assigned charge : 6.500010 assigned positive charge : 407.7894 centred at (gu) : 92.07061 91.11038 92.26616 assigned negative charge : -401.2902 centred at (gu) : 91.91821 90.71420 92.53069 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 26779 mr = 53222 m= 3740 mr = 19002 m= 230 mr = 2107 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1273 time to turn everything in is 0.3700000 number of dielectric boundary points 34423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19725 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) : 0.6368173 object centre at (A) : 13.30550 -0.1925011 27.61850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3680336E-02 6.2803426E-03 midg,1,midg; midg,igrid,midg -1.9438423E-02 2.1250514E-02 1,midg,midg; igrid,midg,midg 1.0647114E-02 2.7965249E-03 gauss-seidel spectral radius is 0.9986561 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 13:05:18 rms-change max change #iterations 4.333626 179.4622 at 10iterations 2.044029 73.68272 at 20iterations 0.9638175 34.27763 at 30iterations 0.4515369 14.38382 at 40iterations 0.2131297 7.176824 at 50iterations 9.9852823E-02 3.313555 at 60iterations 4.7210097E-02 1.558224 at 70iterations 2.2247707E-02 0.6650229 at 80iterations 1.0456023E-02 0.3585300 at 90iterations 4.9524549E-03 0.1471252 at 100iterations 2.3539916E-03 7.1743011E-02 at 110iterations 1.1189578E-03 3.7673950E-02 at 120iterations finished qdiffx linear iterations at : 13:05:32 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.1189578E-03 3.7673950E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:05:32 7.979u 0.209s 0:15.14 53.9% 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 Sat Oct 15 2011 at 13:05:32 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 = 2656 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: 2.865678 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 2.865678 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2512 net assigned charge : 6.500010 assigned positive charge : 407.7894 centred at (gu) : 93.10551 91.66539 93.39903 assigned negative charge : -401.2902 centred at (gu) : 92.87734 91.07113 93.79595 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 180279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 88707 mr = 129083 m= 29639 mr = 71362 m= 6557 mr = 22935 m= 945 mr = 4511 m= 54 mr = 619 m= 0 mr = 7 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 4269 time to turn everything in is 1.070000 number of dielectric boundary points 77664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20096 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) : 1.910452 object centre at (A) : 13.30550 -0.1925011 27.61850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4558906 -0.1144211 midg,1,midg; midg,igrid,midg -0.2996809 0.2265742 1,midg,midg; igrid,midg,midg 0.1900870 -1.7960224E-02 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.380000 now iterating at: 13:05:34 rms-change max change #iterations 10.33364 372.2301 at 10iterations 6.139664 174.4190 at 20iterations 3.599657 75.94278 at 30iterations 2.102854 45.23522 at 40iterations 1.227219 22.57376 at 50iterations 0.7116589 12.52624 at 60iterations 0.4143010 7.670906 at 70iterations 0.2406140 4.449936 at 80iterations 0.1394351 2.713707 at 90iterations 8.0637813E-02 1.523487 at 100iterations 4.6691995E-02 0.8701439 at 110iterations 2.7043726E-02 0.4751596 at 120iterations 1.5603494E-02 0.2935486 at 130iterations 9.0687620E-03 0.1741269 at 140iterations 5.2520004E-03 9.4562531E-02 at 150iterations 3.0633116E-03 5.3283691E-02 at 160iterations 1.7955911E-03 3.3523560E-02 at 170iterations 1.0686065E-03 1.9515991E-02 at 180iterations finished qdiffx linear iterations at : 13:05:48 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 1.0686065E-03 1.9515991E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 13:05:48 15.477u 0.288s 0:16.04 98.1% 0+0k 0+0io 0pf+0w