Sat Oct 8 14:09:23 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 8 2011 at 14:09:23 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6285310 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 0.6285310 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9859911 assigned positive charge : 444.2976 centred at (gu) : 89.14746 89.48173 92.16651 assigned negative charge : -445.2845 centred at (gu) : 89.15160 89.38689 92.09810 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7963 nv = 96 ne = 84 npr = 60987 no. pairs analyzed = 60987 no. exposed pairs = 3459 no. arc points = 23801 no. surface atoms = 1176 nbur = 1786 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4700 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8676094E-09 8.9052596E-09 midg,1,midg; midg,igrid,midg -1.1665374E-08 7.0903421E-09 1,midg,midg; igrid,midg,midg -8.6457891E-10 -1.2724846E-09 gauss-seidel spectral radius is 0.9869183 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 14:09:24 rms-change max change #iterations 0.1470024 22.52367 at 10iterations 1.4439525E-02 1.904144 at 20iterations 1.4916924E-03 0.1979465 at 30iterations 1.8934910E-04 2.5676727E-02 at 40iterations 3.5603971E-05 5.4197311E-03 at 50iterations finished qdiffx linear iterations at : 14:09:28 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 3.5603971E-05 5.4197311E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 14:09:29 5.247u 0.468s 0:06.04 94.3% 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 Sat Oct 8 2011 at 14:09:29 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.885593 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 1.885593 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9859911 assigned positive charge : 444.2976 centred at (gu) : 87.44157 88.44441 96.49890 assigned negative charge : -445.2845 centred at (gu) : 87.45466 88.16066 96.29427 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23801 grid for indexing accessible points = 1.400000 m= 32859 mr = 63614 m= 4798 mr = 24977 m= 241 mr = 2921 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 144 time to turn everything in is 0.7200000 number of dielectric boundary points 33663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22117 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) : 0.6285310 object centre at (A) : 16.09700 32.99400 64.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2796924E-02 8.8538211E-03 midg,1,midg; midg,igrid,midg -5.0224373E-03 1.3482546E-02 1,midg,midg; igrid,midg,midg -1.1519494E-02 7.3633175E-03 gauss-seidel spectral radius is 0.9986405 estimated iterations to convergence 215 setup time was (sec) 1.100000 now iterating at: 14:09:30 rms-change max change #iterations 4.543398 202.9270 at 10iterations 2.133055 71.04094 at 20iterations 1.003519 29.96696 at 30iterations 0.4695887 14.39067 at 40iterations 0.2213095 6.330276 at 50iterations 0.1037327 3.325522 at 60iterations 4.8733130E-02 1.511816 at 70iterations 2.2909695E-02 0.6523542 at 80iterations 1.0817691E-02 0.3317566 at 90iterations 5.0773742E-03 0.1553230 at 100iterations 2.3936688E-03 7.1151733E-02 at 110iterations 1.1288590E-03 3.4002304E-02 at 120iterations finished qdiffx linear iterations at : 14:09:42 total time elapsed so far: 13.30000 # loops : 120 mean,max change (kT/e) : 1.1288590E-03 3.4002304E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 14:09:43 13.481u 0.505s 0:14.28 97.8% 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 Sat Oct 8 2011 at 14:09:43 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.828390 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 2.828390 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9859911 assigned positive charge : 444.2976 centred at (gu) : 86.16225 87.66663 99.74819 assigned negative charge : -445.2845 centred at (gu) : 86.18190 87.24086 99.44147 start vw surface at 0.1200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 202013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23801 grid for indexing accessible points = 1.400000 m= 107100 mr = 153136 m= 38255 mr = 89767 m= 8416 mr = 31156 m= 1001 mr = 6214 m= 37 mr = 621 m= 0 mr = 4 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 476 time to turn everything in is 1.900000 number of dielectric boundary points 75924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 22525 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) : 1.885593 object centre at (A) : 16.09700 32.99400 64.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3980938E-02 0.1312578 midg,1,midg; midg,igrid,midg -2.3452425E-02 0.1654201 1,midg,midg; igrid,midg,midg 1.1439959E-02 0.2670209 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 2.290000 now iterating at: 14:09:46 rms-change max change #iterations 10.62123 377.9292 at 10iterations 6.231127 135.6175 at 20iterations 3.623944 73.72063 at 30iterations 2.108664 39.77449 at 40iterations 1.222611 22.09752 at 50iterations 0.7065968 13.35295 at 60iterations 0.4096946 6.921935 at 70iterations 0.2364610 4.299944 at 80iterations 0.1366889 2.359535 at 90iterations 7.8960612E-02 1.426506 at 100iterations 4.5573737E-02 0.7370882 at 110iterations 2.6235797E-02 0.4477139 at 120iterations 1.5123362E-02 0.2552261 at 130iterations 8.7318458E-03 0.1453261 at 140iterations 5.0561489E-03 9.1075897E-02 at 150iterations 2.9188339E-03 5.0765991E-02 at 160iterations 1.6932744E-03 2.9371262E-02 at 170iterations 9.8786631E-04 1.7274857E-02 at 180iterations finished qdiffx linear iterations at : 14:10:05 total time elapsed so far: 21.45000 # loops : 180 mean,max change (kT/e) : 9.8786631E-04 1.7274857E-02 energy calculations done at 21.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.61000 DelPhi exited at 14:10:06 21.614u 0.569s 0:22.47 98.6% 0+0k 0+0io 0pf+0w