Sat Oct 15 14:45:01 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 Sat Oct 15 2011 at 14:45:01 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIT 107 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: 0.5604093 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): 1.370000 64.89500 ymin,ymax (A): 11.76200 58.96200 zmin,zma (A): -7.232000 42.58800 x,y,z range (A): 63.52500 47.20000 49.82000 scale (grids/A): 0.5604093 object centre (A): 33.13250 35.36200 17.67800 number of atom coordinates read : 2775 total number of charged atoms : 2636 net assigned charge : -1.485974 assigned positive charge : 417.5293 centred at (gu) : 89.12997 89.94854 88.90075 assigned negative charge : -419.0163 centred at (gu) : 89.08547 90.11454 88.80658 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5711 nv = 96 ne = 84 npr = 55499 no. pairs analyzed = 55499 no. exposed pairs = 3619 no. arc points = 25475 no. surface atoms = 1213 nbur = 1562 mkacc time = 0.1000000 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= 243 mr = 2897 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2100000 number of dielectric boundary points 3050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2631 ## 344 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7408 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5066907E-09 6.4239081E-10 midg,1,midg; midg,igrid,midg 1.5980991E-09 -1.9096120E-09 1,midg,midg; igrid,midg,midg -7.6091661E-10 2.6204608E-10 gauss-seidel spectral radius is 0.9835615 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 14:45:03 rms-change max change #iterations 7.9084881E-02 12.34848 at 10iterations 5.6773340E-03 1.008932 at 20iterations 4.0877963E-04 6.8538666E-02 at 30iterations 2.9776280E-05 4.6834946E-03 at 40iterations 2.4099479E-06 4.3106079E-04 at 50iterations finished qdiffx linear iterations at : 14:45:10 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 2.4099479E-06 4.3106079E-04 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 14:45:11 3.856u 0.209s 0:10.34 39.1% 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 15 2011 at 14:45:11 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIT 107 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.681228 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): 1.370000 64.89500 ymin,ymax (A): 11.76200 58.96200 zmin,zma (A): -7.232000 42.58800 x,y,z range (A): 63.52500 47.20000 49.82000 scale (grids/A): 1.681228 object centre (A): 33.13250 35.36200 17.67800 number of atom coordinates read : 2775 total number of charged atoms : 2636 net assigned charge : -1.485974 assigned positive charge : 417.5293 centred at (gu) : 87.38900 89.84511 86.70134 assigned negative charge : -419.0163 centred at (gu) : 87.25612 90.34343 86.41946 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25475 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19418 mr = 42551 m= 2036 mr = 13046 m= 62 mr = 894 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.3300000 number of dielectric boundary points 28241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20391 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) : 0.5604093 object centre at (A) : 33.13250 35.36200 17.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9015909E-03 1.8349517E-03 midg,1,midg; midg,igrid,midg 9.7287260E-03 -1.7713517E-02 1,midg,midg; igrid,midg,midg 1.2907315E-03 1.2545678E-02 gauss-seidel spectral radius is 0.9982698 estimated iterations to convergence 191 setup time was (sec) 0.6200000 now iterating at: 14:45:13 rms-change max change #iterations 3.420418 175.7298 at 10iterations 1.450222 59.81985 at 20iterations 0.6180006 21.56590 at 30iterations 0.2623580 9.553940 at 40iterations 0.1116284 3.864262 at 50iterations 4.7365762E-02 1.850377 at 60iterations 2.0170221E-02 0.7282498 at 70iterations 8.5608773E-03 0.2979507 at 80iterations 3.6572150E-03 0.1374331 at 90iterations 1.5545058E-03 5.9059143E-02 at 100iterations 6.6158862E-04 2.4046898E-02 at 110iterations 2.8264042E-04 1.0288239E-02 at 120iterations finished qdiffx linear iterations at : 14:45:33 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 2.8264042E-04 1.0288239E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 14:45:33 9.164u 0.348s 0:22.08 43.0% 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 15 2011 at 14:45:34 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIT 107 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: 2.521842 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): 1.370000 64.89500 ymin,ymax (A): 11.76200 58.96200 zmin,zma (A): -7.232000 42.58800 x,y,z range (A): 63.52500 47.20000 49.82000 scale (grids/A): 2.521842 object centre (A): 33.13250 35.36200 17.67800 number of atom coordinates read : 2775 total number of charged atoms : 2636 net assigned charge : -1.485974 assigned positive charge : 417.5293 centred at (gu) : 86.08325 89.76735 85.05187 assigned negative charge : -419.0163 centred at (gu) : 85.88404 90.51505 84.62922 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 146996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25475 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 66780 mr = 104319 m= 18842 mr = 52287 m= 3093 mr = 13743 m= 224 mr = 1907 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 810 time to turn everything in is 0.8100000 number of dielectric boundary points 63597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21064 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) : 1.681228 object centre at (A) : 33.13250 35.36200 17.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4033575E-02 2.7262960E-02 midg,1,midg; midg,igrid,midg 0.1498829 -0.2135570 1,midg,midg; igrid,midg,midg 8.2667194E-02 0.2724671 gauss-seidel spectral radius is 0.9991612 estimated iterations to convergence 273 setup time was (sec) 1.070000 now iterating at: 14:45:37 rms-change max change #iterations 8.761135 281.4642 at 10iterations 4.933211 117.4454 at 20iterations 2.760437 72.00180 at 30iterations 1.542613 38.67375 at 40iterations 0.8595074 19.95358 at 50iterations 0.4780414 9.735764 at 60iterations 0.2658849 5.952038 at 70iterations 0.1473539 3.244864 at 80iterations 8.1837408E-02 1.677198 at 90iterations 4.5277763E-02 0.9488525 at 100iterations 2.5103869E-02 0.5364730 at 110iterations 1.3871890E-02 0.2911987 at 120iterations 7.6954300E-03 0.1574059 at 130iterations 4.2663296E-03 9.6191406E-02 at 140iterations 2.3577791E-03 4.6200752E-02 at 150iterations 1.3024436E-03 2.5387764E-02 at 160iterations 7.2103395E-04 1.4512300E-02 at 170iterations 3.9909690E-04 8.3732605E-03 at 180iterations finished qdiffx linear iterations at : 14:46:15 total time elapsed so far: 14.84000 # loops : 180 mean,max change (kT/e) : 3.9909690E-04 8.3732605E-03 energy calculations done at 14.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.97000 DelPhi exited at 14:46:16 14.970u 0.286s 0:41.58 36.6% 0+0k 0+0io 0pf+0w