Sat Oct 8 23:38:29 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 Sat Oct 8 2011 at 23:38:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: WAT 1 has a net charge of 0.4170 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: 0.6219645 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 0.6219645 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.917030 assigned positive charge : 375.0610 centred at (gu) : 88.64537 89.65961 89.80566 assigned negative charge : -365.1448 centred at (gu) : 88.68761 89.75962 89.93861 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6768 nv = 96 ne = 84 npr = 50658 no. pairs analyzed = 50658 no. exposed pairs = 3363 no. arc points = 23439 no. surface atoms = 1127 nbur = 1427 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3587 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7781952E-08 -4.9537080E-10 midg,1,midg; midg,igrid,midg 1.6069253E-08 1.6053936E-09 1,midg,midg; igrid,midg,midg 1.4973585E-08 4.2285984E-09 gauss-seidel spectral radius is 0.9866164 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 23:38:30 rms-change max change #iterations 0.1258039 17.44202 at 10iterations 1.1740751E-02 1.585865 at 20iterations 1.1908390E-03 0.1658878 at 30iterations 2.0069549E-04 3.2810211E-02 at 40iterations 5.2056686E-05 8.7032318E-03 at 50iterations finished qdiffx linear iterations at : 23:38:33 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.2056686E-05 8.7032318E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 23:38:33 3.373u 0.170s 0:03.90 90.7% 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 Sat Oct 8 2011 at 23:38:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: WAT 1 has a net charge of 0.4170 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.865893 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 1.865893 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.917030 assigned positive charge : 375.0610 centred at (gu) : 85.93568 88.97842 89.41656 assigned negative charge : -365.1448 centred at (gu) : 86.06277 89.27891 89.81599 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23439 grid for indexing accessible points = 1.400000 m= 27128 mr = 49087 m= 4562 mr = 19771 m= 239 mr = 2905 m= 0 mr = 60 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 32422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18986 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) : 0.6219645 object centre at (A) : 112.4840 -85.45150 95.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7628358E-02 -8.7975860E-03 midg,1,midg; midg,igrid,midg 2.2295048E-02 -7.1136787E-04 1,midg,midg; igrid,midg,midg 4.7966879E-02 5.1315930E-02 gauss-seidel spectral radius is 0.9985850 estimated iterations to convergence 211 setup time was (sec) 0.6000000 now iterating at: 23:38:34 rms-change max change #iterations 3.971531 164.3232 at 10iterations 1.833858 60.87824 at 20iterations 0.8442745 29.04790 at 30iterations 0.3915511 13.14956 at 40iterations 0.1807249 5.468549 at 50iterations 8.3440259E-02 2.968984 at 60iterations 3.8472492E-02 1.257471 at 70iterations 1.7941063E-02 0.6462402 at 80iterations 8.2874075E-03 0.2964211 at 90iterations 3.8766866E-03 0.1415370 at 100iterations 1.8251552E-03 5.8044434E-02 at 110iterations 8.7437755E-04 3.2011509E-02 at 120iterations finished qdiffx linear iterations at : 23:38:42 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 8.7437755E-04 3.2011509E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 23:38:43 8.533u 0.220s 0:09.17 95.4% 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 Sat Oct 8 2011 at 23:38:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: WAT 1 has a net charge of 0.4170 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.798840 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 2.798840 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.917030 assigned positive charge : 375.0610 centred at (gu) : 83.90341 88.46755 89.12456 assigned negative charge : -365.1448 centred at (gu) : 84.09418 88.91833 89.72392 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23439 grid for indexing accessible points = 1.400000 m= 85547 mr = 118703 m= 33074 mr = 69254 m= 8305 mr = 26626 m= 1099 mr = 6246 m= 59 mr = 718 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 73109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19324 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) : 1.865893 object centre at (A) : 112.4840 -85.45150 95.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5087359 -0.3303325 midg,1,midg; midg,igrid,midg 0.2320729 -4.6710201E-02 1,midg,midg; igrid,midg,midg 0.6559130 0.8005225 gauss-seidel spectral radius is 0.9992543 estimated iterations to convergence 289 setup time was (sec) 1.210000 now iterating at: 23:38:44 rms-change max change #iterations 9.519600 358.5913 at 10iterations 5.612270 138.5262 at 20iterations 3.274085 71.72961 at 30iterations 1.905578 40.60390 at 40iterations 1.102866 21.76796 at 50iterations 0.6376295 11.64025 at 60iterations 0.3667201 8.151563 at 70iterations 0.2118292 4.166475 at 80iterations 0.1217872 2.329690 at 90iterations 7.0055053E-02 1.392525 at 100iterations 4.0203582E-02 0.7659063 at 110iterations 2.3185249E-02 0.4191666 at 120iterations 1.3307462E-02 0.2432189 at 130iterations 7.6411231E-03 0.1515503 at 140iterations 4.3884623E-03 8.1386566E-02 at 150iterations 2.5207209E-03 4.6569824E-02 at 160iterations 1.4531552E-03 2.9935837E-02 at 170iterations 8.4174925E-04 1.5018463E-02 at 180iterations finished qdiffx linear iterations at : 23:38:55 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 8.4174925E-04 1.5018463E-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) 12.46000 DelPhi exited at 23:38:56 12.467u 0.241s 0:13.18 96.3% 0+0k 0+0io 0pf+0w