Mon Oct 10 14:01:55 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 Mon Oct 10 2011 at 14:01:56 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5849 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: 0.5028178 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): 3.758000 74.55900 ymin,ymax (A): 18.58400 85.51100 zmin,zma (A): 6.458000 75.20400 x,y,z range (A): 70.80099 66.92700 68.74600 scale (grids/A): 0.5028178 object centre (A): 39.15850 52.04750 40.83100 number of atom coordinates read : 5849 total number of charged atoms : 5679 net assigned charge : -5.499973 assigned positive charge : 881.7520 centred at (gu) : 89.88574 88.89079 89.05679 assigned negative charge : -887.2597 centred at (gu) : 89.83464 88.88531 89.01479 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9222 nv = 96 ne = 84 npr = 118279 no. pairs analyzed = 118279 no. exposed pairs = 7267 no. arc points = 49988 no. surface atoms = 2444 nbur = 3405 mkacc time = 0.2000000 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= 307 mr = 4783 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4100000 number of dielectric boundary points 4740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4848 ## 739 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 12520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9369177E-10 3.2355389E-11 midg,1,midg; midg,igrid,midg -8.8454688E-11 -3.0833738E-11 1,midg,midg; igrid,midg,midg -1.7681447E-10 6.0973476E-11 gauss-seidel spectral radius is 0.9798486 estimated iterations to convergence 58 setup time was (sec) 0.6000000 now iterating at: 14:01:56 rms-change max change #iterations 7.0702739E-02 9.283638 at 10iterations 3.9315405E-03 0.6098680 at 20iterations 3.7749199E-04 7.6705933E-02 at 30iterations 9.3410890E-05 2.0687103E-02 at 40iterations 2.8339264E-05 5.9947968E-03 at 50iterations finished qdiffx linear iterations at : 14:01:59 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 2.8339264E-05 5.9947968E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:02:00 3.650u 0.159s 0:04.25 89.4% 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 Mon Oct 10 2011 at 14:02:00 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5849 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: 1.508453 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): 3.758000 74.55900 ymin,ymax (A): 18.58400 85.51100 zmin,zma (A): 6.458000 75.20400 x,y,z range (A): 70.80099 66.92700 68.74600 scale (grids/A): 1.508453 object centre (A): 39.15850 52.04750 40.83100 number of atom coordinates read : 5849 total number of charged atoms : 5679 net assigned charge : -5.499973 assigned positive charge : 881.7520 centred at (gu) : 89.65501 86.67050 87.16885 assigned negative charge : -887.2597 centred at (gu) : 89.50367 86.65572 87.04395 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 105227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 29396 mr = 72418 m= 2238 mr = 19225 m= 38 mr = 947 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 674 time to turn everything in is 0.5000000 number of dielectric boundary points 44309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 734 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 42496 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) : 0.5028178 object centre at (A) : 39.15850 52.04750 40.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3632939E-02 -8.5936198E-03 midg,1,midg; midg,igrid,midg -6.3808816E-03 -4.6736551E-03 1,midg,midg; igrid,midg,midg -7.8554256E-03 8.6383671E-03 gauss-seidel spectral radius is 0.9981404 estimated iterations to convergence 184 setup time was (sec) 0.7200000 now iterating at: 14:02:01 rms-change max change #iterations 4.136951 156.0932 at 10iterations 1.711467 58.30875 at 20iterations 0.7064456 22.51019 at 30iterations 0.2919328 8.985968 at 40iterations 0.1208405 4.205498 at 50iterations 5.0026461E-02 1.454815 at 60iterations 2.0717971E-02 0.6775274 at 70iterations 8.6176228E-03 0.2534399 at 80iterations 3.5810266E-03 0.1057243 at 90iterations 1.5017234E-03 4.4048309E-02 at 100iterations 6.4155553E-04 2.1200180E-02 at 110iterations 2.8492909E-04 9.8571777E-03 at 120iterations finished qdiffx linear iterations at : 14:02:08 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.8492909E-04 9.8571777E-03 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 14:02:08 7.956u 0.213s 0:08.52 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 Mon Oct 10 2011 at 14:02:08 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5849 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.262680 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): 3.758000 74.55900 ymin,ymax (A): 18.58400 85.51100 zmin,zma (A): 6.458000 75.20400 x,y,z range (A): 70.80099 66.92700 68.74600 scale (grids/A): 2.262680 object centre (A): 39.15850 52.04750 40.83100 number of atom coordinates read : 5849 total number of charged atoms : 5679 net assigned charge : -5.499973 assigned positive charge : 881.7520 centred at (gu) : 89.48216 85.00533 85.75272 assigned negative charge : -887.2597 centred at (gu) : 89.25540 84.98350 85.56589 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 245884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 107504 mr = 178925 m= 24986 mr = 82896 m= 3044 mr = 17724 m= 119 mr = 1891 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2283 time to turn everything in is 1.210000 number of dielectric boundary points 100064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 45254 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) : 1.508453 object centre at (A) : 39.15850 52.04750 40.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3712537 -0.1891740 midg,1,midg; midg,igrid,midg -0.1628451 -5.5182122E-02 1,midg,midg; igrid,midg,midg 4.0942663E-03 0.1320646 gauss-seidel spectral radius is 0.9991975 estimated iterations to convergence 279 setup time was (sec) 1.460000 now iterating at: 14:02:10 rms-change max change #iterations 11.39771 297.6215 at 10iterations 6.641080 154.8389 at 20iterations 3.841707 77.22726 at 30iterations 2.204041 47.69054 at 40iterations 1.266454 24.46872 at 50iterations 0.7255800 13.47186 at 60iterations 0.4129386 7.889756 at 70iterations 0.2352113 4.416614 at 80iterations 0.1335024 2.420145 at 90iterations 7.5648785E-02 1.483478 at 100iterations 4.2847782E-02 0.7901769 at 110iterations 2.4299586E-02 0.4443188 at 120iterations 1.3719640E-02 0.2585473 at 130iterations 7.7497079E-03 0.1314421 at 140iterations 4.3944684E-03 8.6561203E-02 at 150iterations 2.4803490E-03 4.1702747E-02 at 160iterations 1.4010366E-03 2.3353577E-02 at 170iterations 7.9412939E-04 1.3887405E-02 at 180iterations finished qdiffx linear iterations at : 14:02:22 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 7.9412939E-04 1.3887405E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 14:02:23 13.208u 0.218s 0:14.36 93.3% 0+0k 0+0io 0pf+0w