Mon Oct 10 09:11:36 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 09:11:36 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1042 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: 0.7277634 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): -9.931999 27.41500 ymin,ymax (A): 0.5350000 41.76100 zmin,zma (A): -18.04800 30.86900 x,y,z range (A): 37.34700 41.22600 48.91700 scale (grids/A): 0.7277634 object centre (A): 8.741501 21.14800 6.410500 number of atom coordinates read : 1042 total number of charged atoms : 916 net assigned charge : 1.500003 assigned positive charge : 144.3130 centred at (gu) : 88.21384 91.94225 88.74310 assigned negative charge : -142.8130 centred at (gu) : 88.38402 92.08562 89.04559 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4050 nv = 96 ne = 84 npr = 20251 no. pairs analyzed = 20251 no. exposed pairs = 1562 no. arc points = 11527 no. surface atoms = 524 nbur = 518 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 1930 m= 5 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 5.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 941 ## 89 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 3944 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5468420E-07 -7.0318634E-08 midg,1,midg; midg,igrid,midg 4.7149108E-08 -4.7666671E-08 1,midg,midg; igrid,midg,midg 1.0899575E-07 -2.9214052E-08 gauss-seidel spectral radius is 0.9900651 estimated iterations to convergence 82 setup time was (sec) 0.3700000 now iterating at: 09:11:37 rms-change max change #iterations 0.1480434 28.94074 at 10iterations 1.9015241E-02 3.886642 at 20iterations 2.3570808E-03 0.4221954 at 30iterations 3.0102153E-04 5.0499916E-02 at 40iterations 3.8869810E-05 7.0610046E-03 at 50iterations finished qdiffx linear iterations at : 09:11:39 total time elapsed so far: 2.740000 # loops : 50 mean,max change (kT/e) : 3.8869810E-05 7.0610046E-03 energy calculations done at 2.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.900000 DelPhi exited at 09:11:40 2.908u 0.156s 0:03.34 91.3% 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 09:11:40 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1042 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: 2.183290 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): -9.931999 27.41500 ymin,ymax (A): 0.5350000 41.76100 zmin,zma (A): -18.04800 30.86900 x,y,z range (A): 37.34700 41.22600 48.91700 scale (grids/A): 2.183290 object centre (A): 8.741501 21.14800 6.410500 number of atom coordinates read : 1042 total number of charged atoms : 916 net assigned charge : 1.500003 assigned positive charge : 144.3130 centred at (gu) : 84.64157 95.82693 86.22933 assigned negative charge : -142.8130 centred at (gu) : 85.15202 96.25693 87.13665 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 41432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11527 grid for indexing accessible points = 1.400000 m= 16107 mr = 25349 m= 3742 mr = 11749 m= 419 mr = 2507 m= 12 mr = 174 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 0.3400000 number of dielectric boundary points 21933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7291 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) : 0.7277634 object centre at (A) : 8.741501 21.14800 6.410500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0614469E-02 -1.1740259E-03 midg,1,midg; midg,igrid,midg 1.4368209E-02 9.7680958E-03 1,midg,midg; igrid,midg,midg 1.2991891E-03 -8.1293471E-03 gauss-seidel spectral radius is 0.9987962 estimated iterations to convergence 228 setup time was (sec) 0.5800000 now iterating at: 09:11:40 rms-change max change #iterations 3.169109 178.8570 at 10iterations 1.535053 84.09118 at 20iterations 0.7508227 33.60636 at 30iterations 0.3657381 13.70856 at 40iterations 0.1786267 7.169312 at 50iterations 8.7141953E-02 3.614429 at 60iterations 4.2326495E-02 1.675049 at 70iterations 2.0665977E-02 0.8843080 at 80iterations 1.0113146E-02 0.4181404 at 90iterations 4.9299528E-03 0.1826611 at 100iterations 2.4075056E-03 9.4024658E-02 at 110iterations 1.1834825E-03 5.0641060E-02 at 120iterations finished qdiffx linear iterations at : 09:11:46 total time elapsed so far: 6.410000 # loops : 120 mean,max change (kT/e) : 1.1834825E-03 5.0641060E-02 energy calculations done at 6.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.600000 DelPhi exited at 09:11:47 6.607u 0.180s 0:07.15 94.8% 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 Mon Oct 10 2011 at 09:11:47 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1042 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: 3.274935 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): -9.931999 27.41500 ymin,ymax (A): 0.5350000 41.76100 zmin,zma (A): -18.04800 30.86900 x,y,z range (A): 37.34700 41.22600 48.91700 scale (grids/A): 3.274935 object centre (A): 8.741501 21.14800 6.410500 number of atom coordinates read : 1042 total number of charged atoms : 916 net assigned charge : 1.500003 assigned positive charge : 144.3130 centred at (gu) : 81.96234 98.74041 84.34396 assigned negative charge : -142.8130 centred at (gu) : 82.72802 99.38541 85.70498 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 94877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11527 grid for indexing accessible points = 1.400000 m= 47948 mr = 61536 m= 21691 mr = 38149 m= 7377 mr = 17711 m= 1638 mr = 5721 m= 244 mr = 1099 m= 13 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 49443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 7328 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) : 2.183290 object centre at (A) : 8.741501 21.14800 6.410500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1429448 9.5012439E-03 midg,1,midg; midg,igrid,midg 0.1072724 6.7173794E-02 1,midg,midg; igrid,midg,midg -2.1431535E-02 -3.1235160E-02 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 09:11:48 rms-change max change #iterations 7.207236 313.6727 at 10iterations 4.214725 128.4910 at 20iterations 2.450814 65.47266 at 30iterations 1.430374 37.05098 at 40iterations 0.8288204 19.17418 at 50iterations 0.4811253 11.32865 at 60iterations 0.2775161 6.700283 at 70iterations 0.1608053 4.133836 at 80iterations 9.2935480E-02 2.430365 at 90iterations 5.3829066E-02 1.361816 at 100iterations 3.1019030E-02 0.7600725 at 110iterations 1.7948821E-02 0.4040623 at 120iterations 1.0388202E-02 0.2374144 at 130iterations 6.0035731E-03 0.1440115 at 140iterations 3.4614436E-03 7.6674938E-02 at 150iterations 2.0079280E-03 4.8170567E-02 at 160iterations 1.1588595E-03 2.5039673E-02 at 170iterations 6.7024271E-04 1.6326904E-02 at 180iterations finished qdiffx linear iterations at : 09:11:57 total time elapsed so far: 10.45000 # loops : 180 mean,max change (kT/e) : 6.7024271E-04 1.6326904E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 09:11:58 10.632u 0.174s 0:11.13 97.0% 0+0k 0+0io 0pf+0w