Mon Oct 10 10:19:22 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 Mon Oct 10 2011 at 10:19:22 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5771632 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 0.5771632 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 10.91402 assigned positive charge : 410.9630 centred at (gu) : 91.97174 91.75793 86.90834 assigned negative charge : -400.0495 centred at (gu) : 92.06471 91.78368 86.68130 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6341 nv = 96 ne = 84 npr = 53153 no. pairs analyzed = 53153 no. exposed pairs = 4009 no. arc points = 29578 no. surface atoms = 1338 nbur = 1440 mkacc time = 8.9999996E-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 = 1.484000 m= 318 mr = 2911 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2971 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0042423E-09 3.0360048E-09 midg,1,midg; midg,igrid,midg 1.8478739E-09 2.7653115E-09 1,midg,midg; igrid,midg,midg 2.4931133E-09 9.6979480E-10 gauss-seidel spectral radius is 0.9845086 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 10:19:22 rms-change max change #iterations 9.2432410E-02 15.48943 at 10iterations 6.9727595E-03 1.051079 at 20iterations 5.4646039E-04 8.4356308E-02 at 30iterations 4.7373796E-05 8.2454681E-03 at 40iterations 5.6181516E-06 7.0476532E-04 at 50iterations finished qdiffx linear iterations at : 10:19:25 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.6181516E-06 7.0476532E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:19:26 3.408u 0.178s 0:03.84 92.9% 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 Mon Oct 10 2011 at 10:19:26 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.731489 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 1.731489 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 10.91402 assigned positive charge : 410.9630 centred at (gu) : 95.91482 95.27335 80.72449 assigned negative charge : -400.0495 centred at (gu) : 96.19384 95.35103 80.04364 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29578 grid for indexing accessible points = 1.400000 m= 22096 mr = 42784 m= 2862 mr = 14438 m= 114 mr = 1342 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 34782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20375 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) : 0.5771632 object centre at (A) : 8.860500 15.82300 25.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2913406E-03 1.3578258E-02 midg,1,midg; midg,igrid,midg 1.8216809E-02 2.8147815E-02 1,midg,midg; igrid,midg,midg -4.7925790E-03 1.2140470E-02 gauss-seidel spectral radius is 0.9983814 estimated iterations to convergence 197 setup time was (sec) 0.5500000 now iterating at: 10:19:26 rms-change max change #iterations 3.557657 170.0110 at 10iterations 1.537261 54.96256 at 20iterations 0.6710884 25.92383 at 30iterations 0.2925685 9.807274 at 40iterations 0.1273359 4.928417 at 50iterations 5.5823807E-02 2.045143 at 60iterations 2.4214918E-02 0.9140692 at 70iterations 1.0577816E-02 0.3936577 at 80iterations 4.6295053E-03 0.1558905 at 90iterations 2.0202794E-03 7.6477051E-02 at 100iterations 8.8048773E-04 3.0158043E-02 at 110iterations 3.8533745E-04 1.3292313E-02 at 120iterations finished qdiffx linear iterations at : 10:19:34 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 3.8533745E-04 1.3292313E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 10:19:34 7.771u 0.213s 0:08.25 96.7% 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 Mon Oct 10 2011 at 10:19:34 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.597234 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 2.597234 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 10.91402 assigned positive charge : 410.9630 centred at (gu) : 98.87202 97.91012 76.08662 assigned negative charge : -400.0495 centred at (gu) : 99.29076 98.02654 75.06554 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 157928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29578 grid for indexing accessible points = 1.400000 m= 72362 mr = 105232 m= 23833 mr = 55023 m= 4738 mr = 17303 m= 411 mr = 2989 m= 18 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 78566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 21048 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) : 1.731489 object centre at (A) : 8.860500 15.82300 25.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1523427 0.1446558 midg,1,midg; midg,igrid,midg 0.2929447 0.3409778 1,midg,midg; igrid,midg,midg -0.3526760 0.2261914 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.080000 now iterating at: 10:19:35 rms-change max change #iterations 9.177177 362.8528 at 10iterations 5.360240 158.6103 at 20iterations 3.093130 97.76579 at 30iterations 1.773855 46.38834 at 40iterations 1.011727 25.19092 at 50iterations 0.5744199 15.16069 at 60iterations 0.3257670 7.368347 at 70iterations 0.1844276 4.218673 at 80iterations 0.1041240 2.856311 at 90iterations 5.8712866E-02 1.673332 at 100iterations 3.3118237E-02 0.7674284 at 110iterations 1.8616125E-02 0.4132061 at 120iterations 1.0472863E-02 0.1992111 at 130iterations 5.9081158E-03 0.1257477 at 140iterations 3.3220714E-03 6.8210602E-02 at 150iterations 1.8642978E-03 3.9350510E-02 at 160iterations 1.0513671E-03 2.3874402E-02 at 170iterations 5.9073651E-04 1.1511803E-02 at 180iterations finished qdiffx linear iterations at : 10:19:47 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 5.9073651E-04 1.1511803E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 10:19:47 12.541u 0.210s 0:13.09 97.4% 0+0k 0+0io 0pf+0w