Tue Oct 11 08:20:48 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 Tue Oct 11 2011 at 08:20:48 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: HIR 301 has a net charge of 0.5140 !!! WARNING: HIQ 353 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5885465 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 0.5885465 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.457984 assigned positive charge : 575.1519 centred at (gu) : 90.31313 89.82671 90.57529 assigned negative charge : -577.6122 centred at (gu) : 90.17632 89.81857 90.51138 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8359 nv = 96 ne = 84 npr = 76955 no. pairs analyzed = 76955 no. exposed pairs = 4276 no. arc points = 29728 no. surface atoms = 1449 nbur = 2295 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 = 1.456000 m= 390 mr = 4706 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3500000 number of dielectric boundary points 4012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3093 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7877769E-09 1.8967130E-09 midg,1,midg; midg,igrid,midg -1.1001549E-09 -4.2521903E-10 1,midg,midg; igrid,midg,midg -5.5865748E-09 4.6810076E-09 gauss-seidel spectral radius is 0.9851540 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 08:20:48 rms-change max change #iterations 0.1255136 17.06277 at 10iterations 1.0201726E-02 1.419330 at 20iterations 8.3769031E-04 0.1151428 at 30iterations 6.9724905E-05 1.0467529E-02 at 40iterations 6.1714377E-06 8.2206726E-04 at 50iterations finished qdiffx linear iterations at : 08:20:51 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 6.1714377E-06 8.2206726E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 08:20:52 3.177u 0.159s 0:04.09 81.1% 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 Tue Oct 11 2011 at 08:20:52 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: HIR 301 has a net charge of 0.5140 !!! WARNING: HIQ 353 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.765640 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 1.765640 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.457984 assigned positive charge : 575.1519 centred at (gu) : 90.93777 89.47886 91.72456 assigned negative charge : -577.6122 centred at (gu) : 90.52829 89.45506 91.53368 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29728 grid for indexing accessible points = 1.400000 m= 30520 mr = 66506 m= 3786 mr = 22331 m= 146 mr = 2225 m= 0 mr = 37 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3656 time to turn everything in is 0.6200000 number of dielectric boundary points 36819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 28173 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) : 0.5885465 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0206179E-02 2.6336065E-02 midg,1,midg; midg,igrid,midg -3.9117923E-03 1.9964846E-03 1,midg,midg; igrid,midg,midg -3.5227749E-02 1.4187745E-04 gauss-seidel spectral radius is 0.9985220 estimated iterations to convergence 206 setup time was (sec) 0.8800000 now iterating at: 08:20:53 rms-change max change #iterations 4.588846 180.4439 at 10iterations 2.084853 66.68282 at 20iterations 0.9479259 29.40261 at 30iterations 0.4308127 12.97697 at 40iterations 0.1956778 5.408247 at 50iterations 8.8767618E-02 2.608749 at 60iterations 4.0338885E-02 1.200131 at 70iterations 1.8341247E-02 0.5167232 at 80iterations 8.3650080E-03 0.2326641 at 90iterations 3.7938270E-03 0.1082230 at 100iterations 1.7270114E-03 5.0592899E-02 at 110iterations 7.8548054E-04 2.3970127E-02 at 120iterations finished qdiffx linear iterations at : 08:20:59 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 7.8548054E-04 2.3970127E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 08:21:00 7.028u 0.176s 0:07.83 91.8% 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 Tue Oct 11 2011 at 08:21:00 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3744 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: HIR 301 has a net charge of 0.5140 !!! WARNING: HIQ 353 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.648459 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): 14.97300 75.46100 ymin,ymax (A): -48.61900 9.901000 zmin,zma (A): 74.41400 132.7870 x,y,z range (A): 60.48800 58.52000 58.37299 scale (grids/A): 2.648459 object centre (A): 45.21700 -19.35900 103.6005 number of atom coordinates read : 3744 total number of charged atoms : 3622 net assigned charge : -2.457984 assigned positive charge : 575.1519 centred at (gu) : 91.40646 89.21802 92.58647 assigned negative charge : -577.6122 centred at (gu) : 90.79234 89.18256 92.30059 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 217282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29728 grid for indexing accessible points = 1.400000 m= 104326 mr = 161743 m= 32718 mr = 85676 m= 6484 mr = 25893 m= 625 mr = 4714 m= 19 mr = 354 m= 0 mr = 6 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 12273 time to turn everything in is 1.490000 number of dielectric boundary points 83068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 28969 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) : 1.765640 object centre at (A) : 45.21700 -19.35900 103.6005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1284863 0.4098886 midg,1,midg; midg,igrid,midg -2.3731107E-03 -7.4846982E-03 1,midg,midg; igrid,midg,midg -0.4914477 -0.1967326 gauss-seidel spectral radius is 0.9992511 estimated iterations to convergence 288 setup time was (sec) 1.770000 now iterating at: 08:21:02 rms-change max change #iterations 11.10617 290.6677 at 10iterations 6.464224 149.9247 at 20iterations 3.729423 75.47746 at 30iterations 2.150397 49.29053 at 40iterations 1.237785 24.74301 at 50iterations 0.7102429 11.55412 at 60iterations 0.4077509 7.652328 at 70iterations 0.2334661 4.047565 at 80iterations 0.1339324 2.560471 at 90iterations 7.6499633E-02 1.342281 at 100iterations 4.3903697E-02 0.7726173 at 110iterations 2.5110848E-02 0.4326153 at 120iterations 1.4357961E-02 0.2486935 at 130iterations 8.2310708E-03 0.1402712 at 140iterations 4.7078561E-03 7.9559326E-02 at 150iterations 2.6948957E-03 4.3254852E-02 at 160iterations 1.5420328E-03 2.6237488E-02 at 170iterations 8.8353228E-04 1.4244080E-02 at 180iterations finished qdiffx linear iterations at : 08:21:11 total time elapsed so far: 11.47000 # loops : 180 mean,max change (kT/e) : 8.8353228E-04 1.4244080E-02 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 08:21:12 11.650u 0.178s 0:12.29 96.1% 0+0k 0+0io 0pf+0w