Tue Oct 11 06:00:40 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 06:00:40 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7078801 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 0.7078801 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 89.21960 90.19295 90.25746 assigned negative charge : -320.2010 centred at (gu) : 89.35272 90.13147 90.33753 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7250 nv = 96 ne = 84 npr = 42319 no. pairs analyzed = 42319 no. exposed pairs = 2601 no. arc points = 17669 no. surface atoms = 893 nbur = 1434 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4197 m= 1 mr = 102 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 0.2700000 number of dielectric boundary points 3438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1634 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6502446E-08 9.1319148E-09 midg,1,midg; midg,igrid,midg 1.7909064E-08 8.4591925E-08 1,midg,midg; igrid,midg,midg 1.3687863E-07 -1.5813352E-08 gauss-seidel spectral radius is 0.9896015 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:00:41 rms-change max change #iterations 0.2047111 38.18212 at 10iterations 2.5828572E-02 3.813616 at 20iterations 3.5753762E-03 0.4647675 at 30iterations 6.8015349E-04 8.4751129E-02 at 40iterations 1.9324549E-04 2.4608612E-02 at 50iterations finished qdiffx linear iterations at : 06:00:43 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.9324549E-04 2.4608612E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 06:00:44 3.255u 0.190s 0:03.83 89.8% 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 06:00:44 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.123640 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 2.123640 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 87.65874 90.57896 90.77224 assigned negative charge : -320.2010 centred at (gu) : 88.05824 90.39442 91.01264 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17669 grid for indexing accessible points = 1.400000 m= 31490 mr = 54807 m= 6194 mr = 24121 m= 597 mr = 4211 m= 20 mr = 322 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15840 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) : 0.7078801 object centre at (A) : 49.07500 6.441500 25.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8997185E-02 2.6072277E-02 midg,1,midg; midg,igrid,midg 3.9323434E-02 2.4135921E-02 1,midg,midg; igrid,midg,midg 4.5426685E-02 -4.8846487E-02 gauss-seidel spectral radius is 0.9988379 estimated iterations to convergence 232 setup time was (sec) 0.8900000 now iterating at: 06:00:45 rms-change max change #iterations 4.687111 169.2373 at 10iterations 2.322080 76.39864 at 20iterations 1.155264 38.93123 at 30iterations 0.5749916 18.23417 at 40iterations 0.2866850 8.372709 at 50iterations 0.1426908 4.313393 at 60iterations 7.0986234E-02 2.124580 at 70iterations 3.5544790E-02 1.107071 at 80iterations 1.7796990E-02 0.5597534 at 90iterations 8.9872209E-03 0.2600174 at 100iterations 4.5854608E-03 0.1290808 at 110iterations 2.4180219E-03 7.3669434E-02 at 120iterations finished qdiffx linear iterations at : 06:00:51 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.4180219E-03 7.3669434E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 06:00:52 7.469u 0.196s 0:08.35 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 Tue Oct 11 2011 at 06:00:52 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.185461 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 3.185461 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 86.48806 90.86828 91.15845 assigned negative charge : -320.2010 centred at (gu) : 87.08742 90.59166 91.51910 start vw surface at 0.1500000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 177266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17669 grid for indexing accessible points = 1.400000 m= 97708 mr = 132093 m= 40155 mr = 81568 m= 11842 mr = 33274 m= 2501 mr = 9320 m= 293 mr = 1858 m= 18 mr = 197 m= 0 mr = 2 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 71471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 15968 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) : 2.123640 object centre at (A) : 49.07500 6.441500 25.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1022257 0.2183691 midg,1,midg; midg,igrid,midg 0.3106201 0.1162116 1,midg,midg; igrid,midg,midg 0.4341480 -0.6146174 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 2.110000 now iterating at: 06:00:55 rms-change max change #iterations 10.41614 354.7763 at 10iterations 6.172952 132.9440 at 20iterations 3.655834 78.73824 at 30iterations 2.158635 45.96251 at 40iterations 1.271400 27.05869 at 50iterations 0.7484096 14.27447 at 60iterations 0.4398800 8.224466 at 70iterations 0.2589932 4.526429 at 80iterations 0.1519351 2.634435 at 90iterations 8.9265123E-02 1.615229 at 100iterations 5.2582514E-02 0.9127769 at 110iterations 3.1071682E-02 0.5587692 at 120iterations 1.8528055E-02 0.3144121 at 130iterations 1.1245715E-02 0.2007227 at 140iterations 7.0293490E-03 0.1279373 at 150iterations 4.5674099E-03 8.5006714E-02 at 160iterations 3.1550964E-03 5.7472229E-02 at 170iterations 2.3142118E-03 4.0763855E-02 at 180iterations finished qdiffx linear iterations at : 06:01:05 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 2.3142118E-03 4.0763855E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 06:01:05 12.528u 0.232s 0:13.08 97.4% 0+0k 0+0io 0pf+0w