Mon Oct 10 09:14:37 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 Mon Oct 10 2011 at 09:14:37 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6554238 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 0.6554238 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.26361 92.74076 89.95395 assigned negative charge : -284.8263 centred at (gu) : 90.36620 92.87172 89.89493 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5758 nv = 96 ne = 84 npr = 40597 no. pairs analyzed = 40597 no. exposed pairs = 2467 no. arc points = 17183 no. surface atoms = 829 nbur = 1135 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 3199 m= 7 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1700000 number of dielectric boundary points 2824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1723 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4105957E-10 1.4615679E-08 midg,1,midg; midg,igrid,midg 1.3487226E-08 -1.8051233E-08 1,midg,midg; igrid,midg,midg 1.9145217E-08 -6.3717449E-09 gauss-seidel spectral radius is 0.9878777 estimated iterations to convergence 74 setup time was (sec) 0.3400000 now iterating at: 09:14:37 rms-change max change #iterations 0.1357161 25.62411 at 10iterations 1.3884269E-02 1.982025 at 20iterations 1.4635316E-03 0.2110357 at 30iterations 1.5037856E-04 2.3025393E-02 at 40iterations 1.5833892E-05 2.3002625E-03 at 50iterations finished qdiffx linear iterations at : 09:14:40 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5833892E-05 2.3002625E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:14:40 3.380u 0.185s 0:03.83 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 Mon Oct 10 2011 at 09:14:41 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.966271 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 1.966271 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.79104 98.22210 89.86179 assigned negative charge : -284.8263 centred at (gu) : 91.09882 98.61539 89.68492 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 61657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17183 grid for indexing accessible points = 1.400000 m= 22890 mr = 42570 m= 3696 mr = 17549 m= 229 mr = 2551 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1672 time to turn everything in is 0.3400000 number of dielectric boundary points 25709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14455 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) : 0.6554238 object centre at (A) : 15.10300 22.26700 3.688001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4834317E-02 1.3647638E-02 midg,1,midg; midg,igrid,midg 4.6479449E-02 -3.8313167E-03 1,midg,midg; igrid,midg,midg 7.2026737E-03 -6.6823154E-03 gauss-seidel spectral radius is 0.9986373 estimated iterations to convergence 215 setup time was (sec) 0.5600000 now iterating at: 09:14:41 rms-change max change #iterations 3.783268 194.3040 at 10iterations 1.779195 74.48956 at 20iterations 0.8337890 28.74460 at 30iterations 0.3886688 13.11976 at 40iterations 0.1830183 6.282838 at 50iterations 8.5354596E-02 3.407845 at 60iterations 4.0169653E-02 1.356308 at 70iterations 1.8814685E-02 0.5991353 at 80iterations 8.7866411E-03 0.3189888 at 90iterations 4.1205026E-03 0.1500225 at 100iterations 1.9276678E-03 6.6281438E-02 at 110iterations 9.0124435E-04 3.0117989E-02 at 120iterations finished qdiffx linear iterations at : 09:14:48 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 9.0124435E-04 3.0117989E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 09:14:49 7.834u 0.172s 0:08.38 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 Mon Oct 10 2011 at 09:14:49 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.949407 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 2.949407 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.18666 102.3331 89.79283 assigned negative charge : -284.8263 centred at (gu) : 91.64832 102.9231 89.52736 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 142072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17183 grid for indexing accessible points = 1.400000 m= 73231 mr = 102843 m= 28032 mr = 60882 m= 7050 mr = 23471 m= 1105 mr = 5597 m= 67 mr = 816 m= 0 mr = 22 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5891 time to turn everything in is 0.8000000 number of dielectric boundary points 57926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 14656 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) : 1.966271 object centre at (A) : 15.10300 22.26700 3.688001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.225398 3.1123409E-02 midg,1,midg; midg,igrid,midg 0.4881210 -0.1140194 1,midg,midg; igrid,midg,midg 3.5425901E-02 -4.2069323E-02 gauss-seidel spectral radius is 0.9992472 estimated iterations to convergence 288 setup time was (sec) 1.030000 now iterating at: 09:14:50 rms-change max change #iterations 8.771019 328.9906 at 10iterations 5.021929 114.3975 at 20iterations 2.869215 57.36462 at 30iterations 1.638763 32.30634 at 40iterations 0.9375487 18.00561 at 50iterations 0.5344995 10.82164 at 60iterations 0.3044547 6.425545 at 70iterations 0.1736443 3.540423 at 80iterations 9.9145152E-02 2.149162 at 90iterations 5.6589857E-02 1.080429 at 100iterations 3.2183181E-02 0.6576939 at 110iterations 1.8394483E-02 0.3546660 at 120iterations 1.0482103E-02 0.1971130 at 130iterations 5.9867641E-03 0.1192055 at 140iterations 3.4192402E-03 6.6061974E-02 at 150iterations 1.9467234E-03 4.2831421E-02 at 160iterations 1.1130603E-03 2.0885468E-02 at 170iterations 6.3477189E-04 1.1942208E-02 at 180iterations finished qdiffx linear iterations at : 09:15:01 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 6.3477189E-04 1.1942208E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 09:15:02 12.293u 0.210s 0:12.86 97.2% 0+0k 0+0io 0pf+0w