Mon Oct 10 14:08:45 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 14:08:45 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 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: 0.6158744 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): 3.471000 61.27500 ymin,ymax (A): 4.749000 61.12200 zmin,zma (A): 6.552000 54.26800 x,y,z range (A): 57.80400 56.37300 47.71600 scale (grids/A): 0.6158744 object centre (A): 32.37300 32.93550 30.41000 number of atom coordinates read : 2478 total number of charged atoms : 2308 net assigned charge : 8.500013 assigned positive charge : 368.7670 centred at (gu) : 90.40258 90.87616 91.74497 assigned negative charge : -360.2674 centred at (gu) : 90.37197 90.94034 91.74741 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6268 nv = 96 ne = 84 npr = 49403 no. pairs analyzed = 49403 no. exposed pairs = 3345 no. arc points = 24344 no. surface atoms = 1112 nbur = 1366 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3147 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2333 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2573070E-09 8.6038296E-09 midg,1,midg; midg,igrid,midg 7.8560101E-09 2.9891911E-09 1,midg,midg; igrid,midg,midg 4.0082448E-09 8.3975973E-09 gauss-seidel spectral radius is 0.9863442 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 14:08:46 rms-change max change #iterations 0.1200413 24.92166 at 10iterations 1.0612809E-02 1.828467 at 20iterations 9.5543830E-04 0.1405144 at 30iterations 8.8357898E-05 1.1985779E-02 at 40iterations 8.7394419E-06 1.5201569E-03 at 50iterations finished qdiffx linear iterations at : 14:08:49 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 8.7394419E-06 1.5201569E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 14:08:49 3.514u 0.176s 0:03.99 92.2% 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 14:08:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 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: 1.847623 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): 3.471000 61.27500 ymin,ymax (A): 4.749000 61.12200 zmin,zma (A): 6.552000 54.26800 x,y,z range (A): 57.80400 56.37300 47.71600 scale (grids/A): 1.847623 object centre (A): 32.37300 32.93550 30.41000 number of atom coordinates read : 2478 total number of charged atoms : 2308 net assigned charge : 8.500013 assigned positive charge : 368.7670 centred at (gu) : 91.20761 92.62776 95.23447 assigned negative charge : -360.2674 centred at (gu) : 91.11567 92.82057 95.24202 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24344 grid for indexing accessible points = 1.400000 m= 22506 mr = 45031 m= 3001 mr = 15501 m= 180 mr = 1504 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.5300000 number of dielectric boundary points 31721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18065 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) : 0.6158744 object centre at (A) : 32.37300 32.93550 30.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4316387E-02 3.2734599E-02 midg,1,midg; midg,igrid,midg 4.7028858E-02 4.1728534E-04 1,midg,midg; igrid,midg,midg -1.4471239E-02 -7.1929098E-05 gauss-seidel spectral radius is 0.9985443 estimated iterations to convergence 208 setup time was (sec) 0.8500000 now iterating at: 14:08:51 rms-change max change #iterations 3.821580 177.9009 at 10iterations 1.745736 67.68188 at 20iterations 0.7954838 27.82664 at 30iterations 0.3616883 12.29026 at 40iterations 0.1652309 5.764359 at 50iterations 7.5570777E-02 2.656038 at 60iterations 3.4493044E-02 1.232849 at 70iterations 1.5783703E-02 0.5225949 at 80iterations 7.1998648E-03 0.2662034 at 90iterations 3.2804504E-03 0.1203151 at 100iterations 1.4993332E-03 4.9604416E-02 at 110iterations 6.8372028E-04 2.4673462E-02 at 120iterations finished qdiffx linear iterations at : 14:08:58 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 6.8372028E-04 2.4673462E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 14:08:58 8.121u 0.216s 0:08.64 96.4% 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 14:08:58 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 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: 2.771435 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): 3.471000 61.27500 ymin,ymax (A): 4.749000 61.12200 zmin,zma (A): 6.552000 54.26800 x,y,z range (A): 57.80400 56.37300 47.71600 scale (grids/A): 2.771435 object centre (A): 32.37300 32.93550 30.41000 number of atom coordinates read : 2478 total number of charged atoms : 2308 net assigned charge : 8.500013 assigned positive charge : 368.7670 centred at (gu) : 91.81125 93.94154 97.85155 assigned negative charge : -360.2674 centred at (gu) : 91.67340 94.23100 97.86288 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 157525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24344 grid for indexing accessible points = 1.400000 m= 74690 mr = 110032 m= 24184 mr = 58795 m= 5008 mr = 18051 m= 649 mr = 3285 m= 37 mr = 339 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 184 time to turn everything in is 1.310000 number of dielectric boundary points 71587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 18457 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) : 1.847623 object centre at (A) : 32.37300 32.93550 30.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1453936 0.3590780 midg,1,midg; midg,igrid,midg 0.8707008 3.6826922E-04 1,midg,midg; igrid,midg,midg -6.6016033E-02 -5.5494830E-02 gauss-seidel spectral radius is 0.9992352 estimated iterations to convergence 285 setup time was (sec) 1.630000 now iterating at: 14:09:00 rms-change max change #iterations 9.173905 258.9121 at 10iterations 5.368224 136.7774 at 20iterations 3.113916 71.45928 at 30iterations 1.793392 44.03422 at 40iterations 1.031459 23.61272 at 50iterations 0.5902811 14.33720 at 60iterations 0.3389559 6.867119 at 70iterations 0.1936654 3.839409 at 80iterations 0.1104820 2.696339 at 90iterations 6.3052230E-02 1.253319 at 100iterations 3.6023527E-02 0.7543538 at 110iterations 2.0467386E-02 0.4852648 at 120iterations 1.1676815E-02 0.2336369 at 130iterations 6.6383514E-03 0.1233830 at 140iterations 3.7809308E-03 7.4554443E-02 at 150iterations 2.1524797E-03 4.9057007E-02 at 160iterations 1.2236028E-03 2.2150040E-02 at 170iterations 6.9748424E-04 1.3397217E-02 at 180iterations finished qdiffx linear iterations at : 14:09:11 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 6.9748424E-04 1.3397217E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 14:09:12 13.229u 0.241s 0:14.07 95.6% 0+0k 0+0io 0pf+0w