Tue Oct 11 06:25:11 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 06:25:11 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: HIT 40 has a net charge of 0.5140 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6591493 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 0.6591493 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2001 net assigned charge : 5.959011 assigned positive charge : 329.1249 centred at (gu) : 88.95059 90.59779 90.24845 assigned negative charge : -323.1660 centred at (gu) : 88.96392 90.68038 90.15165 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6134 nv = 96 ne = 84 npr = 43189 no. pairs analyzed = 43189 no. exposed pairs = 2536 no. arc points = 17622 no. surface atoms = 874 nbur = 1261 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3434 m= 3 mr = 44 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 0.1800000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1770 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3788609E-10 3.1844618E-08 midg,1,midg; midg,igrid,midg 2.4763395E-08 1.4761172E-09 1,midg,midg; igrid,midg,midg 2.1004849E-08 1.0298050E-08 gauss-seidel spectral radius is 0.9880213 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 06:25:11 rms-change max change #iterations 0.1531352 28.07587 at 10iterations 1.6851675E-02 2.451668 at 20iterations 2.0668583E-03 0.3157101 at 30iterations 3.6525691E-04 4.7794342E-02 at 40iterations 9.3116432E-05 1.3271332E-02 at 50iterations finished qdiffx linear iterations at : 06:25:14 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 9.3116432E-05 1.3271332E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 06:25:15 3.380u 0.163s 0:03.91 90.5% 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 06:25:15 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: HIT 40 has a net charge of 0.5140 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 1.977448 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 1.977448 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2001 net assigned charge : 5.959011 assigned positive charge : 329.1249 centred at (gu) : 86.85178 91.79339 90.74563 assigned negative charge : -323.1660 centred at (gu) : 86.89186 92.04121 90.45490 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 23916 mr = 46193 m= 3669 mr = 17738 m= 233 mr = 2254 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 27139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15760 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) : 0.6591493 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1951897E-02 2.2115249E-02 midg,1,midg; midg,igrid,midg 2.2197342E-02 5.8556232E-03 1,midg,midg; igrid,midg,midg 6.9531269E-02 7.8786556E-03 gauss-seidel spectral radius is 0.9986746 estimated iterations to convergence 218 setup time was (sec) 0.5600000 now iterating at: 06:25:15 rms-change max change #iterations 4.173819 225.2666 at 10iterations 1.981209 73.39422 at 20iterations 0.9409667 33.62727 at 30iterations 0.4450573 16.07248 at 40iterations 0.2103925 7.012922 at 50iterations 0.1001077 3.183916 at 60iterations 4.7534667E-02 1.729160 at 70iterations 2.2529731E-02 0.7453785 at 80iterations 1.0802809E-02 0.3577347 at 90iterations 5.1863515E-03 0.2059708 at 100iterations 2.5214043E-03 7.9883575E-02 at 110iterations 1.2438622E-03 4.1370392E-02 at 120iterations finished qdiffx linear iterations at : 06:25:22 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.2438622E-03 4.1370392E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 06:25:23 7.730u 0.193s 0:08.31 95.3% 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 06:25:23 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: HIT 40 has a net charge of 0.5140 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.966172 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 2.966172 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2001 net assigned charge : 5.959011 assigned positive charge : 329.1249 centred at (gu) : 85.27753 92.68996 91.11843 assigned negative charge : -323.1660 centred at (gu) : 85.33774 93.06181 90.68229 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 151570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 77446 mr = 111630 m= 27758 mr = 63697 m= 6626 mr = 22391 m= 991 mr = 4900 m= 72 mr = 724 m= 0 mr = 33 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 61088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 16008 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) : 1.977448 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2182466 0.2363084 midg,1,midg; midg,igrid,midg 0.2257532 4.8823062E-02 1,midg,midg; igrid,midg,midg 1.000529 -0.2795909 gauss-seidel spectral radius is 0.9992560 estimated iterations to convergence 289 setup time was (sec) 1.100000 now iterating at: 06:25:24 rms-change max change #iterations 9.569128 381.8579 at 10iterations 5.596101 132.8660 at 20iterations 3.262410 77.70644 at 30iterations 1.901221 40.86996 at 40iterations 1.105707 22.79696 at 50iterations 0.6387030 12.26857 at 60iterations 0.3710895 8.345243 at 70iterations 0.2142597 4.467266 at 80iterations 0.1237639 2.404312 at 90iterations 7.1365036E-02 1.360993 at 100iterations 4.1325103E-02 0.7749386 at 110iterations 2.4000991E-02 0.4662037 at 120iterations 1.3980176E-02 0.2922440 at 130iterations 8.2544973E-03 0.1678944 at 140iterations 4.9569723E-03 9.9006653E-02 at 150iterations 3.0690152E-03 6.2740326E-02 at 160iterations 1.9839823E-03 4.0370941E-02 at 170iterations 1.3501224E-03 2.4616241E-02 at 180iterations finished qdiffx linear iterations at : 06:25:35 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 1.3501224E-03 2.4616241E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 06:25:36 12.293u 0.205s 0:12.98 96.2% 0+0k 0+0io 0pf+0w