Sun Oct 9 19:01:26 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 Sun Oct 9 2011 at 19:01:26 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5488153 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 0.5488153 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.3789420 assigned positive charge : 823.8497 centred at (gu) : 88.27322 89.19555 89.20558 assigned negative charge : -824.2353 centred at (gu) : 88.15470 89.22160 89.13768 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10455 nv = 96 ne = 84 npr = 109987 no. pairs analyzed = 109987 no. exposed pairs = 6165 no. arc points = 42248 no. surface atoms = 2091 nbur = 3283 mkacc time = 0.1900000 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 = 1.568000 m= 481 mr = 6008 m= 0 mr = 36 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4265 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1250825E-09 7.6088835E-10 midg,1,midg; midg,igrid,midg 4.4693488E-10 -2.8224054E-10 1,midg,midg; igrid,midg,midg -2.5192686E-09 1.0432283E-09 gauss-seidel spectral radius is 0.9830519 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 19:01:27 rms-change max change #iterations 0.1062194 12.16849 at 10iterations 9.9780904E-03 1.545265 at 20iterations 2.9660058E-03 0.3224106 at 30iterations 1.3381819E-03 0.1635265 at 40iterations 6.2785536E-04 8.2047939E-02 at 50iterations finished qdiffx linear iterations at : 19:01:30 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 6.2785536E-04 8.2047939E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 19:01:30 3.605u 0.177s 0:04.08 92.4% 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 Sun Oct 9 2011 at 19:01:30 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.646446 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 1.646446 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.3789420 assigned positive charge : 823.8497 centred at (gu) : 84.81812 87.58520 87.61536 assigned negative charge : -824.2353 centred at (gu) : 84.46413 87.66470 87.41311 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 117298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 40401 mr = 85367 m= 4712 mr = 29313 m= 136 mr = 2545 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.5800000 number of dielectric boundary points 45311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 39927 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) : 0.5488153 object centre at (A) : 35.68850 22.16050 31.22700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0138254E-02 1.4734437E-02 midg,1,midg; midg,igrid,midg 1.8125372E-02 8.0476273E-03 1,midg,midg; igrid,midg,midg -2.9354353E-02 7.2529176E-03 gauss-seidel spectral radius is 0.9984274 estimated iterations to convergence 200 setup time was (sec) 0.7900000 now iterating at: 19:01:31 rms-change max change #iterations 4.896842 168.2358 at 10iterations 2.167033 64.67155 at 20iterations 0.9647409 26.36217 at 30iterations 0.4276488 11.50657 at 40iterations 0.1900424 5.325317 at 50iterations 8.4987804E-02 2.230208 at 60iterations 3.8385637E-02 1.121868 at 70iterations 1.7758407E-02 0.4904652 at 80iterations 8.7434482E-03 0.2557526 at 90iterations 4.8260726E-03 0.1353493 at 100iterations 3.0323088E-03 8.7211609E-02 at 110iterations 2.1227759E-03 5.4912567E-02 at 120iterations finished qdiffx linear iterations at : 19:01:39 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.1227759E-03 5.4912567E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 19:01:39 8.290u 0.200s 0:08.78 96.6% 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 19:01:39 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.469669 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 2.469669 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.3789420 assigned positive charge : 823.8497 centred at (gu) : 82.22704 86.37737 86.42255 assigned negative charge : -824.2353 centred at (gu) : 81.69606 86.49699 86.11961 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 273058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 136966 mr = 207977 m= 42742 mr = 112098 m= 7638 mr = 33137 m= 567 mr = 5239 m= 8 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 1.430000 number of dielectric boundary points 102220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 41678 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) : 1.646446 object centre at (A) : 35.68850 22.16050 31.22700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4773033 0.3558738 midg,1,midg; midg,igrid,midg 0.1873937 -2.7529520E-03 1,midg,midg; igrid,midg,midg -0.5197503 6.7409463E-02 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 1.680000 now iterating at: 19:01:41 rms-change max change #iterations 12.40090 324.5417 at 10iterations 7.294498 167.5588 at 20iterations 4.264817 86.43246 at 30iterations 2.482195 46.94758 at 40iterations 1.441508 25.31128 at 50iterations 0.8341150 13.18916 at 60iterations 0.4830716 7.940292 at 70iterations 0.2784055 4.219407 at 80iterations 0.1609109 2.525185 at 90iterations 9.2898116E-02 1.483708 at 100iterations 5.3739838E-02 0.9729276 at 110iterations 3.1174229E-02 0.5271406 at 120iterations 1.8249679E-02 0.2979393 at 130iterations 1.0955241E-02 0.1859512 at 140iterations 6.7910287E-03 0.1131363 at 150iterations 4.4386364E-03 7.3428154E-02 at 160iterations 3.1127138E-03 5.2558780E-02 at 170iterations 2.3420653E-03 3.7906647E-02 at 180iterations finished qdiffx linear iterations at : 19:01:53 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 2.3420653E-03 3.7906647E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 19:01:53 13.777u 0.210s 0:14.30 97.7% 0+0k 0+0io 0pf+0w