Sun Oct 9 14:35:50 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 Sun Oct 9 2011 at 14:35:50 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 0.5686175 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 0.5686175 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 410.7185 centred at (gu) : 89.65549 90.32835 88.48980 assigned negative charge : -404.2745 centred at (gu) : 89.61342 90.22285 88.52734 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5696 nv = 96 ne = 84 npr = 53320 no. pairs analyzed = 53320 no. exposed pairs = 3502 no. arc points = 24919 no. surface atoms = 1178 nbur = 1515 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 246 mr = 2835 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2521 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7268 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0538822E-09 2.9992278E-10 midg,1,midg; midg,igrid,midg -4.8174659E-10 2.5342410E-09 1,midg,midg; igrid,midg,midg 3.7905168E-10 1.3802205E-09 gauss-seidel spectral radius is 0.9840215 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 14:35:50 rms-change max change #iterations 8.6768903E-02 14.21751 at 10iterations 6.6256174E-03 1.208768 at 20iterations 5.7864405E-04 0.1218185 at 30iterations 7.5935081E-05 1.5983582E-02 at 40iterations 1.4542876E-05 3.0479431E-03 at 50iterations finished qdiffx linear iterations at : 14:35:53 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.4542876E-05 3.0479431E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:35:54 3.397u 0.182s 0:03.85 92.7% 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 Sun Oct 9 2011 at 14:35:54 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 1.705852 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 1.705852 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 410.7185 centred at (gu) : 88.96606 90.98448 85.46870 assigned negative charge : -404.2745 centred at (gu) : 88.83984 90.66839 85.58189 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24919 grid for indexing accessible points = 1.400000 m= 19753 mr = 41461 m= 2155 mr = 13329 m= 53 mr = 1003 m= 0 mr = 2 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 28636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19712 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) : 0.5686175 object centre at (A) : 26.17600 15.28800 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7066118E-02 1.1236844E-02 midg,1,midg; midg,igrid,midg -2.0382302E-03 3.9564651E-03 1,midg,midg; igrid,midg,midg -1.1525273E-02 -4.1001022E-04 gauss-seidel spectral radius is 0.9983197 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 14:35:55 rms-change max change #iterations 3.447929 158.4339 at 10iterations 1.481070 53.54243 at 20iterations 0.6385180 24.03521 at 30iterations 0.2759765 10.23744 at 40iterations 0.1186179 4.271154 at 50iterations 5.0991360E-02 1.716089 at 60iterations 2.1956628E-02 0.8164405 at 70iterations 9.5554106E-03 0.3593063 at 80iterations 4.1013202E-03 0.1478977 at 90iterations 1.7723942E-03 6.5585136E-02 at 100iterations 7.7291211E-04 2.6271820E-02 at 110iterations 3.3508069E-04 1.2825012E-02 at 120iterations finished qdiffx linear iterations at : 14:36:02 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 3.3508069E-04 1.2825012E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 14:36:02 7.711u 0.195s 0:08.22 96.1% 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 Sun Oct 9 2011 at 14:36:02 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 2.558779 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 2.558779 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 410.7185 centred at (gu) : 88.44894 91.47663 83.20293 assigned negative charge : -404.2745 centred at (gu) : 88.25964 91.00253 83.37280 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 144938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24919 grid for indexing accessible points = 1.400000 m= 67295 mr = 101707 m= 20026 mr = 52583 m= 3426 mr = 14839 m= 310 mr = 2079 m= 11 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 64681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20363 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) : 1.705852 object centre at (A) : 26.17600 15.28800 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.079718 0.1570239 midg,1,midg; midg,igrid,midg -3.8886830E-02 1.2394930E-02 1,midg,midg; igrid,midg,midg -0.1355346 -1.1612870E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.000000 now iterating at: 14:36:03 rms-change max change #iterations 8.854750 337.1762 at 10iterations 5.094798 134.4979 at 20iterations 2.914177 89.32618 at 30iterations 1.651971 40.47466 at 40iterations 0.9352247 22.78454 at 50iterations 0.5269656 12.96004 at 60iterations 0.2963161 7.168413 at 70iterations 0.1661140 3.367764 at 80iterations 9.2993431E-02 2.005756 at 90iterations 5.2131183E-02 1.101665 at 100iterations 2.9198747E-02 0.6301556 at 110iterations 1.6271956E-02 0.3819084 at 120iterations 9.1119772E-03 0.1894760 at 130iterations 5.0959084E-03 0.1021519 at 140iterations 2.8582097E-03 5.8923721E-02 at 150iterations 1.6054369E-03 3.0897141E-02 at 160iterations 9.0665423E-04 1.8825531E-02 at 170iterations 5.1606575E-04 1.0940552E-02 at 180iterations finished qdiffx linear iterations at : 14:36:14 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 5.1606575E-04 1.0940552E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:36:15 12.274u 0.224s 0:12.76 97.8% 0+0k 0+0io 0pf+0w