Sat Oct 8 11:32:49 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 Sat Oct 8 2011 at 11:32:49 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 = 4371 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: 0.5667526 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 0.5667526 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.999943 assigned positive charge : 657.6401 centred at (gu) : 89.41832 90.23824 89.81544 assigned negative charge : -659.6433 centred at (gu) : 89.62255 90.19481 89.64946 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8936 nv = 96 ne = 84 npr = 91636 no. pairs analyzed = 91636 no. exposed pairs = 4926 no. arc points = 33366 no. surface atoms = 1669 nbur = 2702 mkacc time = 0.1600000 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= 360 mr = 5175 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.3100000 number of dielectric boundary points 4091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3520 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9960235E-09 2.9679277E-09 midg,1,midg; midg,igrid,midg -1.1318030E-09 6.5036798E-10 1,midg,midg; igrid,midg,midg 4.4594244E-09 -4.0433896E-09 gauss-seidel spectral radius is 0.9840357 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 11:32:50 rms-change max change #iterations 0.1069437 17.20905 at 10iterations 8.7454189E-03 1.221104 at 20iterations 1.1853479E-03 0.1527252 at 30iterations 3.3203923E-04 3.9380074E-02 at 40iterations 1.1408688E-04 1.4196396E-02 at 50iterations finished qdiffx linear iterations at : 11:32:53 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.1408688E-04 1.4196396E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 11:32:53 3.612u 0.185s 0:04.14 91.5% 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 Sat Oct 8 2011 at 11:32:53 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 = 4371 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: 1.700258 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 1.700258 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.999943 assigned positive charge : 657.6401 centred at (gu) : 88.25360 90.71344 89.44538 assigned negative charge : -659.6433 centred at (gu) : 88.86710 90.58396 88.94813 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 100228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33366 grid for indexing accessible points = 1.400000 m= 33938 mr = 72571 m= 4257 mr = 25221 m= 123 mr = 2495 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5384 time to turn everything in is 0.4900000 number of dielectric boundary points 38244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 32641 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) : 0.5667526 object centre at (A) : 87.96150 51.68900 23.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7790580E-02 2.5825283E-02 midg,1,midg; midg,igrid,midg -3.1686567E-02 3.6658172E-02 1,midg,midg; igrid,midg,midg 3.8493112E-02 -3.5382055E-02 gauss-seidel spectral radius is 0.9984572 estimated iterations to convergence 202 setup time was (sec) 0.7500000 now iterating at: 11:32:54 rms-change max change #iterations 4.523930 147.6880 at 10iterations 2.024761 64.37576 at 20iterations 0.9071520 27.68973 at 30iterations 0.4052979 11.60647 at 40iterations 0.1813487 5.157425 at 50iterations 8.0975890E-02 2.469207 at 60iterations 3.6386915E-02 1.230312 at 70iterations 1.6375644E-02 0.4601917 at 80iterations 7.3821847E-03 0.2266703 at 90iterations 3.3474755E-03 9.5803261E-02 at 100iterations 1.5545074E-03 4.8022509E-02 at 110iterations 7.4632117E-04 2.1620750E-02 at 120iterations finished qdiffx linear iterations at : 11:33:03 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 7.4632117E-04 2.1620750E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 11:33:03 9.095u 0.276s 0:09.78 95.7% 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 Sat Oct 8 2011 at 11:33:03 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 = 4371 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: 2.550387 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 2.550387 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.999943 assigned positive charge : 657.6401 centred at (gu) : 87.38013 91.06990 89.16770 assigned negative charge : -659.6433 centred at (gu) : 88.30050 90.87575 88.42214 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 232788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33366 grid for indexing accessible points = 1.400000 m= 115257 mr = 176068 m= 36591 mr = 95272 m= 7253 mr = 29129 m= 616 mr = 5358 m= 12 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 17925 time to turn everything in is 1.240000 number of dielectric boundary points 86382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 33772 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) : 1.700258 object centre at (A) : 87.96150 51.68900 23.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3594703 0.2622136 midg,1,midg; midg,igrid,midg -0.8377921 0.7635865 1,midg,midg; igrid,midg,midg 0.6544079 -0.4293303 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 11:33:05 rms-change max change #iterations 11.29125 315.2375 at 10iterations 6.568444 139.5465 at 20iterations 3.797932 67.99758 at 30iterations 2.194813 37.49726 at 40iterations 1.263259 21.74071 at 50iterations 0.7260292 13.56569 at 60iterations 0.4163795 7.045567 at 70iterations 0.2388723 4.374290 at 80iterations 0.1363753 2.461082 at 90iterations 7.8205779E-02 1.390625 at 100iterations 4.4741504E-02 0.7563019 at 110iterations 2.5629783E-02 0.4189339 at 120iterations 1.4703750E-02 0.2257423 at 130iterations 8.4693590E-03 0.1346054 at 140iterations 4.9087717E-03 7.8748703E-02 at 150iterations 2.8942507E-03 5.2192688E-02 at 160iterations 1.7381485E-03 2.9136658E-02 at 170iterations 1.0840180E-03 1.9318581E-02 at 180iterations finished qdiffx linear iterations at : 11:33:18 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 1.0840180E-03 1.9318581E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 11:33:18 14.410u 0.267s 0:15.03 97.6% 0+0k 0+0io 0pf+0w