Tue Oct 11 08:29:13 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 08:29:13 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6536428 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 0.6536428 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2742 net assigned charge : -0.8599817 assigned positive charge : 438.0813 centred at (gu) : 89.41756 90.68071 91.51155 assigned negative charge : -438.9421 centred at (gu) : 89.14982 90.64554 91.46118 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7909 nv = 96 ne = 84 npr = 60453 no. pairs analyzed = 60453 no. exposed pairs = 3432 no. arc points = 23392 no. surface atoms = 1166 nbur = 1729 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4465 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3300000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2200 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1619449E-09 1.0924420E-08 midg,1,midg; midg,igrid,midg -7.2041657E-09 5.8004903E-09 1,midg,midg; igrid,midg,midg -6.0957582E-08 4.2038813E-08 gauss-seidel spectral radius is 0.9878856 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 08:29:14 rms-change max change #iterations 0.1691328 28.15884 at 10iterations 1.7958708E-02 2.232384 at 20iterations 1.9652899E-03 0.3026466 at 30iterations 2.8590488E-04 3.6613464E-02 at 40iterations 6.6186483E-05 1.0416031E-02 at 50iterations finished qdiffx linear iterations at : 08:29:17 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 6.6186483E-05 1.0416031E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 08:29:18 4.201u 0.227s 0:04.76 92.8% 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 08:29:18 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.960928 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 1.960928 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2742 net assigned charge : -0.8599817 assigned positive charge : 438.0813 centred at (gu) : 88.25218 92.04154 94.53376 assigned negative charge : -438.9421 centred at (gu) : 87.44890 91.93597 94.38301 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23392 grid for indexing accessible points = 1.400000 m= 31210 mr = 59417 m= 5156 mr = 23078 m= 296 mr = 3230 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3192 time to turn everything in is 0.7400000 number of dielectric boundary points 35298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21634 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) : 0.6536428 object centre at (A) : 13.80100 -2.391000 17.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3240832E-02 1.1935872E-03 midg,1,midg; midg,igrid,midg -1.0751662E-02 -2.7110489E-02 1,midg,midg; igrid,midg,midg -1.7479779E-02 6.3136883E-02 gauss-seidel spectral radius is 0.9987285 estimated iterations to convergence 222 setup time was (sec) 1.060000 now iterating at: 08:29:19 rms-change max change #iterations 4.805278 198.4953 at 10iterations 2.320171 84.55588 at 20iterations 1.113829 31.71749 at 30iterations 0.5374703 15.04583 at 40iterations 0.2590302 8.423821 at 50iterations 0.1249786 4.216232 at 60iterations 5.9945531E-02 1.915443 at 70iterations 2.8977601E-02 0.8212814 at 80iterations 1.3985225E-02 0.4297829 at 90iterations 6.7405743E-03 0.1903934 at 100iterations 3.2676321E-03 9.3862534E-02 at 110iterations 1.5919735E-03 4.6442032E-02 at 120iterations finished qdiffx linear iterations at : 08:29:28 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 1.5919735E-03 4.6442032E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 08:29:28 9.842u 0.259s 0:10.39 97.1% 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 Tue Oct 11 2011 at 08:29:28 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.941392 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 2.941392 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2742 net assigned charge : -0.8599817 assigned positive charge : 438.0813 centred at (gu) : 87.37794 93.06213 96.80045 assigned negative charge : -438.9421 centred at (gu) : 86.17339 92.90404 96.57437 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 195480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23392 grid for indexing accessible points = 1.400000 m= 100239 mr = 144255 m= 37217 mr = 82081 m= 9167 mr = 29980 m= 1333 mr = 6736 m= 87 mr = 834 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 10685 time to turn everything in is 1.710000 number of dielectric boundary points 79612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 21932 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) : 1.960928 object centre at (A) : 13.80100 -2.391000 17.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4402765 0.3084136 midg,1,midg; midg,igrid,midg -0.1299504 -0.4227992 1,midg,midg; igrid,midg,midg -2.8921751E-02 0.5927776 gauss-seidel spectral radius is 0.9992829 estimated iterations to convergence 295 setup time was (sec) 2.050000 now iterating at: 08:29:31 rms-change max change #iterations 11.09363 421.9968 at 10iterations 6.554607 155.5823 at 20iterations 3.846067 89.34096 at 30iterations 2.258674 43.86098 at 40iterations 1.321693 23.09471 at 50iterations 0.7718385 14.16648 at 60iterations 0.4511562 7.688744 at 70iterations 0.2625807 4.483221 at 80iterations 0.1529596 3.110907 at 90iterations 8.9080207E-02 1.649841 at 100iterations 5.1893152E-02 0.9116344 at 110iterations 3.0109687E-02 0.5085964 at 120iterations 1.7502911E-02 0.2896557 at 130iterations 1.0213187E-02 0.1677855 at 140iterations 5.9562214E-03 0.1059227 at 150iterations 3.4852510E-03 6.2015533E-02 at 160iterations 2.0514370E-03 3.4015656E-02 at 170iterations 1.2250714E-03 2.3750305E-02 at 180iterations finished qdiffx linear iterations at : 08:29:44 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 1.2250714E-03 2.3750305E-02 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 08:29:45 15.920u 0.291s 0:17.18 94.3% 0+0k 0+0io 0pf+0w