Tue Oct 11 00:56:02 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 00:56:03 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 = 2764 !!! WARNING: LEU 299 has a net charge of -0.2720 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: 0.6423790 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): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 0.6423790 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2620 net assigned charge : 6.228014 assigned positive charge : 417.7174 centred at (gu) : 89.27257 89.07154 89.93503 assigned negative charge : -411.4902 centred at (gu) : 89.27170 89.09089 90.24278 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7574 nv = 96 ne = 84 npr = 56028 no. pairs analyzed = 56028 no. exposed pairs = 3276 no. arc points = 23333 no. surface atoms = 1110 nbur = 1654 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 4271 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.3600000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9632273E-08 -3.1782626E-08 midg,1,midg; midg,igrid,midg 1.4883715E-08 5.9384146E-09 1,midg,midg; igrid,midg,midg 1.1149355E-08 8.4623633E-09 gauss-seidel spectral radius is 0.9874564 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 00:56:04 rms-change max change #iterations 0.1545583 22.03180 at 10iterations 1.5891159E-02 2.257811 at 20iterations 1.8631011E-03 0.3191223 at 30iterations 3.3977628E-04 6.6673279E-02 at 40iterations 7.9450860E-05 1.8337250E-02 at 50iterations finished qdiffx linear iterations at : 00:56:07 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 7.9450860E-05 1.8337250E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 00:56:08 4.176u 0.269s 0:05.20 85.1% 0+0k 0+0io 5pf+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 00:56:08 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 = 2764 !!! WARNING: LEU 299 has a net charge of -0.2720 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: 1.927137 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): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 1.927137 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2620 net assigned charge : 6.228014 assigned positive charge : 417.7174 centred at (gu) : 87.81721 87.21432 89.80427 assigned negative charge : -411.4902 centred at (gu) : 87.81485 87.27209 90.72801 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23333 grid for indexing accessible points = 1.400000 m= 29469 mr = 57883 m= 4581 mr = 22107 m= 258 mr = 2992 m= 2 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3961 time to turn everything in is 0.7200000 number of dielectric boundary points 33623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20631 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) : 0.6423790 object centre at (A) : 8.956001 0.7610006 4.725499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9316450E-02 -4.1913915E-02 midg,1,midg; midg,igrid,midg 2.2056862E-03 2.2732884E-02 1,midg,midg; igrid,midg,midg 1.4515599E-02 9.4822189E-03 gauss-seidel spectral radius is 0.9986781 estimated iterations to convergence 218 setup time was (sec) 1.020000 now iterating at: 00:56:09 rms-change max change #iterations 4.530616 173.9639 at 10iterations 2.140121 70.49820 at 20iterations 1.015836 33.61264 at 30iterations 0.4816727 15.09486 at 40iterations 0.2282700 7.049803 at 50iterations 0.1080205 3.257507 at 60iterations 5.1507685E-02 1.625172 at 70iterations 2.4480442E-02 0.7222595 at 80iterations 1.1679322E-02 0.3456612 at 90iterations 5.6293514E-03 0.1623077 at 100iterations 2.7499511E-03 8.7646484E-02 at 110iterations 1.3748958E-03 4.6012878E-02 at 120iterations finished qdiffx linear iterations at : 00:56:18 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 1.3748958E-03 4.6012878E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 00:56:18 9.765u 0.312s 0:10.56 95.3% 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 Tue Oct 11 2011 at 00:56:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: LEU 299 has a net charge of -0.2720 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: 2.890705 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): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 2.890705 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2620 net assigned charge : 6.228014 assigned positive charge : 417.7174 centred at (gu) : 86.72571 85.82119 89.70625 assigned negative charge : -411.4902 centred at (gu) : 86.72208 85.90806 91.09195 start vw surface at 0.1700000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 190399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23333 grid for indexing accessible points = 1.400000 m= 96283 mr = 139785 m= 34359 mr = 79625 m= 8259 mr = 28035 m= 1266 mr = 6368 m= 71 mr = 906 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 12949 time to turn everything in is 1.870000 number of dielectric boundary points 75871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 20959 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) : 1.927137 object centre at (A) : 8.956001 0.7610006 4.725499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9111460 -0.4487835 midg,1,midg; midg,igrid,midg -3.2834284E-02 0.1593905 1,midg,midg; igrid,midg,midg 0.3314780 0.1164442 gauss-seidel spectral radius is 0.9992643 estimated iterations to convergence 291 setup time was (sec) 2.200000 now iterating at: 00:56:21 rms-change max change #iterations 10.39248 442.5615 at 10iterations 6.054831 200.9392 at 20iterations 3.523616 103.7418 at 30iterations 2.041349 44.74855 at 40iterations 1.179396 33.81953 at 50iterations 0.6812635 13.05504 at 60iterations 0.3931298 8.603002 at 70iterations 0.2266084 3.871097 at 80iterations 0.1304114 2.616917 at 90iterations 7.5349823E-02 1.285965 at 100iterations 4.3534551E-02 0.8142729 at 110iterations 2.5071276E-02 0.4415779 at 120iterations 1.4492956E-02 0.2913399 at 130iterations 8.4112193E-03 0.1455196 at 140iterations 4.9097985E-03 9.6286774E-02 at 150iterations 2.9041986E-03 5.4311752E-02 at 160iterations 1.7589362E-03 3.6582947E-02 at 170iterations 1.1066694E-03 2.6515961E-02 at 180iterations finished qdiffx linear iterations at : 00:56:35 total time elapsed so far: 16.42000 # loops : 180 mean,max change (kT/e) : 1.1066694E-03 2.6515961E-02 energy calculations done at 16.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.61000 DelPhi exited at 00:56:36 16.607u 0.303s 0:17.51 96.5% 0+0k 0+0io 0pf+0w