Thu Jan 19 11:43:15 PST 2012 #!/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 Thu Jan 19 2012 at 11:43:19 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 = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5060484 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 0.5060484 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.2360039E-05 assigned positive charge : 880.2184 centred at (gu) : 90.28381 89.12178 89.09286 assigned negative charge : -880.2252 centred at (gu) : 90.35241 89.03219 89.12206 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9665 nv = 96 ne = 84 npr = 112030 no. pairs analyzed = 112030 no. exposed pairs = 7917 no. arc points = 55227 no. surface atoms = 2634 nbur = 3171 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 = 1.680000 m= 335 mr = 4760 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 5234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5337 ## 816 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12905 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0046918E-10 -5.8542116E-11 midg,1,midg; midg,igrid,midg -2.9910271E-10 1.8522038E-10 1,midg,midg; igrid,midg,midg 1.6725325E-10 -1.9371582E-10 gauss-seidel spectral radius is 0.9801206 estimated iterations to convergence 59 setup time was (sec) 0.5700000 now iterating at: 11:43:23 rms-change max change #iterations 6.8790622E-02 10.19977 at 10iterations 4.3812315E-03 0.5959110 at 20iterations 9.2653412E-04 7.6004028E-02 at 30iterations 3.5475011E-04 2.5347233E-02 at 40iterations 1.4078133E-04 1.0152340E-02 at 50iterations finished qdiffx linear iterations at : 11:43:33 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.4078133E-04 1.0152340E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 11:43:34 3.757u 0.178s 0:15.40 25.4% 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 Thu Jan 19 2012 at 11:43:39 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 = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.518145 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 1.518145 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.2360039E-05 assigned positive charge : 880.2184 centred at (gu) : 90.84953 87.36358 87.27703 assigned negative charge : -880.2252 centred at (gu) : 91.05686 87.09630 87.36600 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 109329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 55227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31451 mr = 72956 m= 2475 mr = 20528 m= 45 mr = 917 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.5300000 number of dielectric boundary points 48899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 774 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 42299 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) : 0.5060484 object centre at (A) : 34.37350 36.13350 52.19100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1444092E-03 1.6003627E-02 midg,1,midg; midg,igrid,midg -1.4812655E-03 7.9996726E-03 1,midg,midg; igrid,midg,midg -1.3071285E-03 -1.3935728E-02 gauss-seidel spectral radius is 0.9981908 estimated iterations to convergence 187 setup time was (sec) 0.8200000 now iterating at: 11:43:44 rms-change max change #iterations 4.242709 182.4786 at 10iterations 1.772188 56.99493 at 20iterations 0.7434406 21.37843 at 30iterations 0.3120194 9.766520 at 40iterations 0.1308470 4.073360 at 50iterations 5.5127408E-02 1.735167 at 60iterations 2.3209061E-02 0.6774311 at 70iterations 9.8126223E-03 0.3377600 at 80iterations 4.2051249E-03 0.1334000 at 90iterations 1.8535734E-03 6.4864159E-02 at 100iterations 8.7995763E-04 2.4723053E-02 at 110iterations 4.6324998E-04 1.2002945E-02 at 120iterations finished qdiffx linear iterations at : 11:44:08 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 4.6324998E-04 1.2002945E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 11:44:09 8.783u 0.292s 0:31.00 29.2% 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 Thu Jan 19 2012 at 11:44:11 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 = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.277218 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 2.277218 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.2360039E-05 assigned positive charge : 880.2184 centred at (gu) : 91.27394 86.04487 85.91506 assigned negative charge : -880.2252 centred at (gu) : 91.58504 85.64420 86.04878 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 254527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 55227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112270 mr = 179932 m= 28121 mr = 86309 m= 3316 mr = 20069 m= 111 mr = 1706 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 1358 time to turn everything in is 1.290000 number of dielectric boundary points 110306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 44984 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) : 1.518145 object centre at (A) : 34.37350 36.13350 52.19100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3992189E-02 0.2670527 midg,1,midg; midg,igrid,midg -3.1392910E-02 0.1758073 1,midg,midg; igrid,midg,midg -0.1489853 -0.1388342 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.560000 now iterating at: 11:44:19 rms-change max change #iterations 11.68184 318.8982 at 10iterations 6.913820 176.9184 at 20iterations 4.026352 86.29263 at 30iterations 2.346406 48.66833 at 40iterations 1.360184 25.88096 at 50iterations 0.7861994 15.14280 at 60iterations 0.4541903 7.776440 at 70iterations 0.2607612 5.539528 at 80iterations 0.1493894 2.769042 at 90iterations 8.5576691E-02 1.685600 at 100iterations 4.9076818E-02 0.8504848 at 110iterations 2.8030092E-02 0.5739613 at 120iterations 1.6030172E-02 0.2950706 at 130iterations 9.1610104E-03 0.1538630 at 140iterations 5.2274880E-03 0.1050558 at 150iterations 2.9812769E-03 5.6129456E-02 at 160iterations 1.7032828E-03 3.4149170E-02 at 170iterations 9.7291765E-04 1.8303871E-02 at 180iterations finished qdiffx linear iterations at : 11:44:56 total time elapsed so far: 14.03000 # loops : 180 mean,max change (kT/e) : 9.7291765E-04 1.8303871E-02 energy calculations done at 14.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 11:44:58 14.165u 0.220s 0:47.01 30.5% 0+0k 0+0io 0pf+0w