Tue Oct 11 05:26:28 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 05:26:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6877234 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 0.6877234 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.17692 89.64895 89.36777 assigned negative charge : -303.7472 centred at (gu) : 90.34795 89.66865 89.34199 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 40627 no. pairs analyzed = 40627 no. exposed pairs = 2546 no. arc points = 17186 no. surface atoms = 871 nbur = 1366 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3755 m= 6 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1686 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5489801E-08 4.1784986E-08 midg,1,midg; midg,igrid,midg 4.8606591E-08 3.1173251E-08 1,midg,midg; igrid,midg,midg 8.7680974E-08 -1.4520608E-08 gauss-seidel spectral radius is 0.9889819 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 05:26:29 rms-change max change #iterations 0.1708151 23.26003 at 10iterations 2.0226497E-02 2.934466 at 20iterations 2.5169558E-03 0.3718090 at 30iterations 4.1176545E-04 5.5931091E-02 at 40iterations 9.9941775E-05 1.2714386E-02 at 50iterations finished qdiffx linear iterations at : 05:26:31 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 9.9941775E-05 1.2714386E-02 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 05:26:32 3.199u 0.174s 0:03.70 90.8% 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 05:26:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 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: 2.063170 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 2.063170 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.53087 88.94675 88.10305 assigned negative charge : -303.7472 centred at (gu) : 91.04391 89.00603 88.02590 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 28230 mr = 49684 m= 5346 mr = 21480 m= 450 mr = 3542 m= 7 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15287 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) : 0.6877234 object centre at (A) : 41.59900 15.10600 46.01850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5009267E-02 4.2949643E-02 midg,1,midg; midg,igrid,midg 2.3052249E-02 1.0716756E-02 1,midg,midg; igrid,midg,midg 3.7887812E-02 1.0219587E-02 gauss-seidel spectral radius is 0.9987694 estimated iterations to convergence 226 setup time was (sec) 0.8200000 now iterating at: 05:26:33 rms-change max change #iterations 4.326019 199.5942 at 10iterations 2.116193 70.18195 at 20iterations 1.024023 34.21099 at 30iterations 0.5034505 15.42027 at 40iterations 0.2457136 8.589577 at 50iterations 0.1194738 3.678670 at 60iterations 5.8413651E-02 1.692779 at 70iterations 2.8537646E-02 0.9524307 at 80iterations 1.4021312E-02 0.4713440 at 90iterations 6.8679745E-03 0.2060183 at 100iterations 3.3932230E-03 0.1200452 at 110iterations 1.7093248E-03 5.4168701E-02 at 120iterations finished qdiffx linear iterations at : 05:26:39 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.7093248E-03 5.4168701E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 05:26:40 7.462u 0.204s 0:08.10 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 05:26:40 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 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: 3.094755 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 3.094755 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.79630 88.42008 87.15459 assigned negative charge : -303.7472 centred at (gu) : 91.56598 88.50919 87.03888 start vw surface at 0.1700000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 161638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 88095 mr = 119750 m= 35497 mr = 73303 m= 10021 mr = 29187 m= 1883 mr = 7819 m= 162 mr = 1346 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 65810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 15432 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) : 2.063170 object centre at (A) : 41.59900 15.10600 46.01850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3394894 0.3019312 midg,1,midg; midg,igrid,midg 0.2003611 8.6313821E-02 1,midg,midg; igrid,midg,midg 0.3182909 0.2475065 gauss-seidel spectral radius is 0.9992792 estimated iterations to convergence 294 setup time was (sec) 1.910000 now iterating at: 05:26:42 rms-change max change #iterations 9.771196 484.9177 at 10iterations 5.781949 180.4606 at 20iterations 3.395125 88.22123 at 30iterations 1.992458 41.99781 at 40iterations 1.164300 23.17919 at 50iterations 0.6814178 12.93064 at 60iterations 0.3982973 7.841913 at 70iterations 0.2317495 5.322890 at 80iterations 0.1350859 2.549194 at 90iterations 7.8715503E-02 1.519688 at 100iterations 4.5906924E-02 0.8504234 at 110iterations 2.6875475E-02 0.4966183 at 120iterations 1.5806638E-02 0.3059959 at 130iterations 9.3821278E-03 0.1878471 at 140iterations 5.6785182E-03 0.1045494 at 150iterations 3.5516901E-03 6.2301636E-02 at 160iterations 2.3397661E-03 4.5021534E-02 at 170iterations 1.6324425E-03 3.0426025E-02 at 180iterations finished qdiffx linear iterations at : 05:26:52 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 1.6324425E-03 3.0426025E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 05:26:53 12.404u 0.225s 0:12.93 97.6% 0+0k 0+0io 0pf+0w