Sat Oct 8 11:31:45 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 11:31:45 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 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: 0.5704578 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): -20.61100 26.98500 ymin,ymax (A): -39.57200 1.065000 zmin,zma (A): 126.2180 188.6240 x,y,z range (A): 47.59600 40.63700 62.40601 scale (grids/A): 0.5704578 object centre (A): 3.187000 -19.25350 157.4210 number of atom coordinates read : 1303 total number of charged atoms : 1274 net assigned charge : -3.999995 assigned positive charge : 202.9342 centred at (gu) : 89.44183 89.79487 87.53655 assigned negative charge : -206.9341 centred at (gu) : 89.27349 89.79837 87.81025 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 3132 nv = 96 ne = 84 npr = 20566 no. pairs analyzed = 20566 no. exposed pairs = 2268 no. arc points = 17825 no. surface atoms = 757 nbur = 546 mkacc time = 4.0000007E-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 = 1.512000 m= 149 mr = 1105 m= 0 mr = 5 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1827 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 3889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3977675E-09 -1.5384273E-09 midg,1,midg; midg,igrid,midg -6.6800093E-10 -6.5692213E-10 1,midg,midg; igrid,midg,midg -2.2075144E-09 4.8174315E-10 gauss-seidel spectral radius is 0.9840285 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 11:31:46 rms-change max change #iterations 5.6805249E-02 15.44781 at 10iterations 4.0451195E-03 1.027863 at 20iterations 2.8569042E-04 6.8716288E-02 at 30iterations 2.1181566E-05 5.7334900E-03 at 40iterations 1.4808072E-06 3.6621094E-04 at 50iterations finished qdiffx linear iterations at : 11:31:48 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 1.4808072E-06 3.6621094E-04 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.000000 DelPhi exited at 11:31:49 3.005u 0.150s 0:03.50 90.0% 0+0k 0+0io 6pf+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 11:31:49 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.711374 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): -20.61100 26.98500 ymin,ymax (A): -39.57200 1.065000 zmin,zma (A): 126.2180 188.6240 x,y,z range (A): 47.59600 40.63700 62.40601 scale (grids/A): 1.711374 object centre (A): 3.187000 -19.25350 157.4210 number of atom coordinates read : 1303 total number of charged atoms : 1274 net assigned charge : -3.999995 assigned positive charge : 202.9342 centred at (gu) : 88.32587 89.38463 82.60985 assigned negative charge : -206.9341 centred at (gu) : 87.82050 89.39516 83.43080 start vw surface at 0.1000000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 33069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17825 grid for indexing accessible points = 1.400000 m= 8704 mr = 17248 m= 942 mr = 4851 m= 31 mr = 371 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 20276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9816 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) : 0.5704578 object centre at (A) : 3.187000 -19.25350 157.4210 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4627252E-02 -1.8313836E-02 midg,1,midg; midg,igrid,midg -1.5152189E-04 -3.9846352E-03 1,midg,midg; igrid,midg,midg -7.2889994E-03 -4.8053340E-04 gauss-seidel spectral radius is 0.9981707 estimated iterations to convergence 186 setup time was (sec) 0.5100000 now iterating at: 11:31:50 rms-change max change #iterations 2.368361 153.9160 at 10iterations 0.9694335 51.70040 at 20iterations 0.3976558 22.99141 at 30iterations 0.1631782 8.259901 at 40iterations 6.7111418E-02 3.431654 at 50iterations 2.7546534E-02 1.301831 at 60iterations 1.1317200E-02 0.5815773 at 70iterations 4.6523595E-03 0.2227411 at 80iterations 1.9055958E-03 9.9580526E-02 at 90iterations 7.8616454E-04 4.1767120E-02 at 100iterations 3.2219381E-04 1.5422821E-02 at 110iterations 1.3263721E-04 6.3400269E-03 at 120iterations finished qdiffx linear iterations at : 11:31:59 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 1.3263721E-04 6.3400269E-03 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 11:32:00 6.762u 0.230s 0:11.44 61.1% 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 8 2011 at 11:32:00 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.567060 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): -20.61100 26.98500 ymin,ymax (A): -39.57200 1.065000 zmin,zma (A): 126.2180 188.6240 x,y,z range (A): 47.59600 40.63700 62.40601 scale (grids/A): 2.567060 object centre (A): 3.187000 -19.25350 157.4210 number of atom coordinates read : 1303 total number of charged atoms : 1274 net assigned charge : -3.999995 assigned positive charge : 202.9342 centred at (gu) : 87.48881 89.07701 78.91483 assigned negative charge : -206.9341 centred at (gu) : 86.73089 89.09279 80.14629 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 76320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17825 grid for indexing accessible points = 1.400000 m= 29700 mr = 43368 m= 7921 mr = 20461 m= 1402 mr = 5146 m= 99 mr = 792 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 45648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 10181 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) : 1.711374 object centre at (A) : 3.187000 -19.25350 157.4210 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4967604 -0.1460512 midg,1,midg; midg,igrid,midg 1.4609098E-02 -5.5046830E-02 1,midg,midg; igrid,midg,midg -7.8648254E-02 -3.9285244E-03 gauss-seidel spectral radius is 0.9990964 estimated iterations to convergence 263 setup time was (sec) 0.8200000 now iterating at: 11:32:02 rms-change max change #iterations 6.203862 322.4670 at 10iterations 3.461678 119.5925 at 20iterations 1.901596 57.23146 at 30iterations 1.037614 32.56773 at 40iterations 0.5655944 18.43893 at 50iterations 0.3084044 8.611463 at 60iterations 0.1665999 4.647782 at 70iterations 9.0102971E-02 2.482009 at 80iterations 4.8773173E-02 1.378723 at 90iterations 2.6337214E-02 0.7279129 at 100iterations 1.4242788E-02 0.3867111 at 110iterations 7.6835370E-03 0.2112322 at 120iterations 4.1406471E-03 0.1181488 at 130iterations 2.2330170E-03 6.1294556E-02 at 140iterations 1.2005738E-03 3.4254551E-02 at 150iterations 6.4778433E-04 1.7204285E-02 at 160iterations 3.4999481E-04 9.2633963E-03 at 170iterations 1.8835762E-04 5.0086975E-03 at 180iterations finished qdiffx linear iterations at : 11:32:17 total time elapsed so far: 9.920000 # loops : 180 mean,max change (kT/e) : 1.8835762E-04 5.0086975E-03 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.10000 DelPhi exited at 11:32:17 10.101u 0.240s 0:17.31 59.7% 0+0k 0+0io 0pf+0w