Sat Oct 15 14:05:47 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 Sat Oct 15 2011 at 14:05:47 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4761 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5133826 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 0.5133826 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4511 net assigned charge : 7.706036 assigned positive charge : 715.8556 centred at (gu) : 90.16026 90.46959 88.33383 assigned negative charge : -708.1537 centred at (gu) : 90.05002 90.52360 88.29559 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8007 nv = 96 ne = 84 npr = 95977 no. pairs analyzed = 95977 no. exposed pairs = 6103 no. arc points = 42260 no. surface atoms = 2045 nbur = 2716 mkacc time = 0.1700000 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 = 1.652000 m= 292 mr = 4137 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4057 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9564978E-11 1.5339559E-10 midg,1,midg; midg,igrid,midg 2.4825214E-10 -3.6030880E-11 1,midg,midg; igrid,midg,midg -1.8845449E-10 4.5817963E-10 gauss-seidel spectral radius is 0.9805980 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:05:47 rms-change max change #iterations 7.0362426E-02 10.02740 at 10iterations 4.2940830E-03 0.6587677 at 20iterations 5.5269862E-04 7.8010559E-02 at 30iterations 2.0186158E-04 3.0190796E-02 at 40iterations 8.2311104E-05 1.2169212E-02 at 50iterations finished qdiffx linear iterations at : 14:05:51 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 8.2311104E-05 1.2169212E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 14:05:51 3.840u 0.245s 0:04.39 92.9% 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 14:05:51 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4761 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.540148 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 1.540148 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4511 net assigned charge : 7.706036 assigned positive charge : 715.8556 centred at (gu) : 90.47942 91.40762 85.00008 assigned negative charge : -708.1537 centred at (gu) : 90.14996 91.57073 84.88649 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26209 mr = 62129 m= 2317 mr = 17283 m= 51 mr = 945 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 38849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33967 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) : 0.5133826 object centre at (A) : 9.487000 1.633501 30.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8552734E-03 2.1377223E-02 midg,1,midg; midg,igrid,midg 9.2704277E-03 -1.2304850E-02 1,midg,midg; igrid,midg,midg -1.7741427E-03 1.1453897E-02 gauss-seidel spectral radius is 0.9981382 estimated iterations to convergence 184 setup time was (sec) 0.7000000 now iterating at: 14:05:52 rms-change max change #iterations 3.839513 171.4372 at 10iterations 1.580201 55.24325 at 20iterations 0.6517634 19.90450 at 30iterations 0.2697973 8.410515 at 40iterations 0.1114045 3.690512 at 50iterations 4.6181619E-02 1.395880 at 60iterations 1.9073486E-02 0.7643547 at 70iterations 7.9630977E-03 0.2652316 at 80iterations 3.3349872E-03 0.1128340 at 90iterations 1.4288600E-03 4.1965485E-02 at 100iterations 6.5373152E-04 2.3559570E-02 at 110iterations 3.3777580E-04 1.1535645E-02 at 120iterations finished qdiffx linear iterations at : 14:06:00 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 3.3777580E-04 1.1535645E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 14:06:01 8.627u 0.252s 0:10.06 88.1% 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 14:06:01 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4761 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.310221 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 2.310221 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4511 net assigned charge : 7.706036 assigned positive charge : 715.8556 centred at (gu) : 90.71880 92.11090 82.49969 assigned negative charge : -708.1537 centred at (gu) : 90.22478 92.35591 82.32966 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 211319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94010 mr = 152874 m= 23489 mr = 73145 m= 3254 mr = 16471 m= 194 mr = 1936 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 87775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 36013 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) : 1.540148 object centre at (A) : 9.487000 1.633501 30.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1385575 0.4807124 midg,1,midg; midg,igrid,midg 0.1971832 -0.2705522 1,midg,midg; igrid,midg,midg -2.2653958E-02 0.1577460 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.420000 now iterating at: 14:06:03 rms-change max change #iterations 10.39434 340.8701 at 10iterations 5.994717 131.1513 at 20iterations 3.433042 77.35156 at 30iterations 1.952266 40.10312 at 40iterations 1.104675 27.28127 at 50iterations 0.6233259 13.93742 at 60iterations 0.3509871 7.047012 at 70iterations 0.1975575 4.712424 at 80iterations 0.1107260 2.413970 at 90iterations 6.1941009E-02 1.326606 at 100iterations 3.4688972E-02 0.8187962 at 110iterations 1.9433009E-02 0.4200478 at 120iterations 1.0849146E-02 0.1998820 at 130iterations 6.0900636E-03 0.1155472 at 140iterations 3.4138500E-03 6.6460609E-02 at 150iterations 1.9224503E-03 3.6304474E-02 at 160iterations 1.0946442E-03 2.2033691E-02 at 170iterations 6.3408137E-04 1.3069153E-02 at 180iterations finished qdiffx linear iterations at : 14:06:18 total time elapsed so far: 14.21000 # loops : 180 mean,max change (kT/e) : 6.3408137E-04 1.3069153E-02 energy calculations done at 14.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.35000 DelPhi exited at 14:06:18 14.353u 0.277s 0:17.25 84.7% 0+0k 0+0io 0pf+0w