Tue Oct 11 04:14:21 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 04:14:21 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIR 77 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: 0.6683061 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): -11.06200 36.43000 ymin,ymax (A): 6.786000 55.74100 zmin,zma (A): -7.920000 45.34900 x,y,z range (A): 47.49200 48.95500 53.26900 scale (grids/A): 0.6683061 object centre (A): 12.68400 31.26350 18.71450 number of atom coordinates read : 2770 total number of charged atoms : 2601 net assigned charge : 3.514017 assigned positive charge : 420.9778 centred at (gu) : 90.11003 90.47077 91.50977 assigned negative charge : -417.4643 centred at (gu) : 89.85402 90.33871 91.54856 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8323 nv = 96 ne = 84 npr = 56435 no. pairs analyzed = 56435 no. exposed pairs = 3354 no. arc points = 23431 no. surface atoms = 1130 nbur = 1640 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4806 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.4300000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5687016E-08 1.0318032E-09 midg,1,midg; midg,igrid,midg -2.1622114E-08 4.9930346E-08 1,midg,midg; igrid,midg,midg -5.6422227E-08 7.8234095E-08 gauss-seidel spectral radius is 0.9884051 estimated iterations to convergence 76 setup time was (sec) 0.7000000 now iterating at: 04:14:22 rms-change max change #iterations 0.1840690 24.27723 at 10iterations 2.0545837E-02 3.495506 at 20iterations 2.2586754E-03 0.2593384 at 30iterations 2.5691351E-04 3.5805702E-02 at 40iterations 3.4036166E-05 4.4507980E-03 at 50iterations finished qdiffx linear iterations at : 04:14:25 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.4036166E-05 4.4507980E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 04:14:26 4.065u 0.189s 0:04.62 91.7% 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 04:14:26 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIR 77 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: 2.004918 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): -11.06200 36.43000 ymin,ymax (A): 6.786000 55.74100 zmin,zma (A): -7.920000 45.34900 x,y,z range (A): 47.49200 48.95500 53.26900 scale (grids/A): 2.004918 object centre (A): 12.68400 31.26350 18.71450 number of atom coordinates read : 2770 total number of charged atoms : 2601 net assigned charge : 3.514017 assigned positive charge : 420.9778 centred at (gu) : 90.32969 91.41179 94.52896 assigned negative charge : -417.4643 centred at (gu) : 89.56168 91.01599 94.64555 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 88774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23431 grid for indexing accessible points = 1.400000 m= 35429 mr = 63168 m= 6519 mr = 27215 m= 471 mr = 4300 m= 10 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1312 time to turn everything in is 0.8200000 number of dielectric boundary points 36307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 20556 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) : 0.6683061 object centre at (A) : 12.68400 31.26350 18.71450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5966997E-03 6.1810859E-03 midg,1,midg; midg,igrid,midg -1.1599039E-02 3.3656437E-02 1,midg,midg; igrid,midg,midg -2.1145524E-02 7.0710577E-02 gauss-seidel spectral radius is 0.9987764 estimated iterations to convergence 226 setup time was (sec) 1.160000 now iterating at: 04:14:27 rms-change max change #iterations 4.933150 221.9896 at 10iterations 2.421119 87.24283 at 20iterations 1.179763 35.39776 at 30iterations 0.5761051 15.76661 at 40iterations 0.2812500 7.429376 at 50iterations 0.1373098 3.928780 at 60iterations 6.7189857E-02 1.898727 at 70iterations 3.2890588E-02 0.9520912 at 80iterations 1.6071513E-02 0.4718490 at 90iterations 7.8539839E-03 0.2014465 at 100iterations 3.8360076E-03 0.1082792 at 110iterations 1.8752913E-03 5.2478790E-02 at 120iterations finished qdiffx linear iterations at : 04:14:35 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 1.8752913E-03 5.2478790E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.140000 DelPhi exited at 04:14:36 9.145u 0.189s 0:09.86 94.5% 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 Tue Oct 11 2011 at 04:14:36 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIR 77 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.007377 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): -11.06200 36.43000 ymin,ymax (A): 6.786000 55.74100 zmin,zma (A): -7.920000 45.34900 x,y,z range (A): 47.49200 48.95500 53.26900 scale (grids/A): 3.007377 object centre (A): 12.68400 31.26350 18.71450 number of atom coordinates read : 2770 total number of charged atoms : 2601 net assigned charge : 3.514017 assigned positive charge : 420.9778 centred at (gu) : 90.49431 92.11763 96.79313 assigned negative charge : -417.4643 centred at (gu) : 89.34245 91.52376 96.96814 start vw surface at 0.2200000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 204784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23431 grid for indexing accessible points = 1.400000 m= 110795 mr = 152301 m= 44704 mr = 92544 m= 12071 mr = 36935 m= 2065 mr = 9349 m= 154 mr = 1456 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 4400 time to turn everything in is 2.130000 number of dielectric boundary points 81935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 20808 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) : 2.004918 object centre at (A) : 12.68400 31.26350 18.71450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8425371E-02 0.4039241 midg,1,midg; midg,igrid,midg -0.1314677 0.3935787 1,midg,midg; igrid,midg,midg -0.1241122 0.5621459 gauss-seidel spectral radius is 0.9992936 estimated iterations to convergence 297 setup time was (sec) 2.480000 now iterating at: 04:14:39 rms-change max change #iterations 11.17668 424.1525 at 10iterations 6.587095 153.8978 at 20iterations 3.875211 84.47407 at 30iterations 2.271580 45.22541 at 40iterations 1.334883 25.01473 at 50iterations 0.7808498 13.82923 at 60iterations 0.4568806 8.111434 at 70iterations 0.2671087 5.095375 at 80iterations 0.1561457 2.827286 at 90iterations 9.1247901E-02 1.600834 at 100iterations 5.3228322E-02 0.8760223 at 110iterations 3.1054115E-02 0.5046654 at 120iterations 1.8131567E-02 0.2837365 at 130iterations 1.0572445E-02 0.1737633 at 140iterations 6.1666328E-03 9.8814011E-02 at 150iterations 3.6051762E-03 6.1697960E-02 at 160iterations 2.1133884E-03 3.6749840E-02 at 170iterations 1.2374679E-03 2.1160126E-02 at 180iterations finished qdiffx linear iterations at : 04:14:51 total time elapsed so far: 14.62000 # loops : 180 mean,max change (kT/e) : 1.2374679E-03 2.1160126E-02 energy calculations done at 14.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.86000 DelPhi exited at 04:14:51 14.860u 0.201s 0:15.49 97.2% 0+0k 0+0io 0pf+0w