Sat Oct 8 11:33:18 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 11:33:19 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4371 !!! WARNING: HIR 437 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5667526 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 0.5667526 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.985943 assigned positive charge : 660.0822 centred at (gu) : 89.42476 90.23742 89.81557 assigned negative charge : -662.0713 centred at (gu) : 89.62768 90.19775 89.64939 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8936 nv = 96 ne = 84 npr = 91636 no. pairs analyzed = 91636 no. exposed pairs = 4926 no. arc points = 33366 no. surface atoms = 1669 nbur = 2702 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 = 1.512000 m= 360 mr = 5175 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.3000000 number of dielectric boundary points 4091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3520 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0114361E-09 2.9861369E-09 midg,1,midg; midg,igrid,midg -1.0578985E-09 5.7397254E-10 1,midg,midg; igrid,midg,midg 4.4427546E-09 -4.0364032E-09 gauss-seidel spectral radius is 0.9840357 estimated iterations to convergence 65 setup time was (sec) 0.5000000 now iterating at: 11:33:19 rms-change max change #iterations 0.1085284 17.17179 at 10iterations 8.8489540E-03 1.247057 at 20iterations 1.2304983E-03 0.1572151 at 30iterations 3.5832662E-04 4.3409348E-02 at 40iterations 1.2538780E-04 1.6069412E-02 at 50iterations finished qdiffx linear iterations at : 11:33:22 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.2538780E-04 1.6069412E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 11:33:23 3.666u 0.187s 0:04.20 91.4% 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 11:33:23 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4371 !!! WARNING: HIR 437 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.700258 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 1.700258 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.985943 assigned positive charge : 660.0822 centred at (gu) : 88.27290 90.71098 89.44576 assigned negative charge : -662.0713 centred at (gu) : 88.88248 90.59277 88.94793 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 100228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33366 grid for indexing accessible points = 1.400000 m= 33938 mr = 72571 m= 4257 mr = 25221 m= 123 mr = 2495 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 5384 time to turn everything in is 0.4900000 number of dielectric boundary points 38244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 32641 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) : 0.5667526 object centre at (A) : 87.96150 51.68900 23.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7754596E-02 2.6026800E-02 midg,1,midg; midg,igrid,midg -3.1234244E-02 3.5952836E-02 1,midg,midg; igrid,midg,midg 3.8429368E-02 -3.5296768E-02 gauss-seidel spectral radius is 0.9984572 estimated iterations to convergence 202 setup time was (sec) 0.7200000 now iterating at: 11:33:24 rms-change max change #iterations 4.546004 147.6880 at 10iterations 2.035463 64.37583 at 20iterations 0.9120799 27.68637 at 30iterations 0.4073275 12.28389 at 40iterations 0.1822173 5.339016 at 50iterations 8.1384793E-02 2.530956 at 60iterations 3.6578108E-02 1.220324 at 70iterations 1.6468344E-02 0.4631805 at 80iterations 7.4358243E-03 0.2228370 at 90iterations 3.3829203E-03 0.1019506 at 100iterations 1.5836158E-03 5.0600052E-02 at 110iterations 7.7149988E-04 2.2048950E-02 at 120iterations finished qdiffx linear iterations at : 11:33:32 total time elapsed so far: 8.490000 # loops : 120 mean,max change (kT/e) : 7.7149988E-04 2.2048950E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.630000 DelPhi exited at 11:33:32 8.628u 0.225s 0:09.24 95.6% 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 11:33:32 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4371 !!! WARNING: HIR 437 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.550387 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): 60.12000 115.8030 ymin,ymax (A): 20.31600 83.06200 zmin,zma (A): -7.674000 55.14000 x,y,z range (A): 55.68300 62.74600 62.81400 scale (grids/A): 2.550387 object centre (A): 87.96150 51.68900 23.73300 number of atom coordinates read : 4371 total number of charged atoms : 4224 net assigned charge : -1.985943 assigned positive charge : 660.0822 centred at (gu) : 87.40910 91.06620 89.16825 assigned negative charge : -662.0713 centred at (gu) : 88.32359 90.88895 88.42184 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 232788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33366 grid for indexing accessible points = 1.400000 m= 115257 mr = 176068 m= 36591 mr = 95272 m= 7253 mr = 29129 m= 616 mr = 5358 m= 12 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 17925 time to turn everything in is 1.240000 number of dielectric boundary points 86382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 33772 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) : 1.700258 object centre at (A) : 87.96150 51.68900 23.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3585314 0.2649841 midg,1,midg; midg,igrid,midg -0.8322102 0.7541734 1,midg,midg; igrid,midg,midg 0.6535231 -0.4278482 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 11:33:34 rms-change max change #iterations 11.34083 315.2375 at 10iterations 6.596952 139.3456 at 20iterations 3.813190 69.14790 at 30iterations 2.203684 37.37165 at 40iterations 1.268357 21.54214 at 50iterations 0.7289623 13.63655 at 60iterations 0.4180167 7.090005 at 70iterations 0.2397470 4.414673 at 80iterations 0.1368853 2.472129 at 90iterations 7.8485586E-02 1.376282 at 100iterations 4.4913631E-02 0.7560158 at 110iterations 2.5730392E-02 0.4224825 at 120iterations 1.4769417E-02 0.2267799 at 130iterations 8.5175699E-03 0.1345558 at 140iterations 4.9478970E-03 8.0520630E-02 at 150iterations 2.9306966E-03 5.3066254E-02 at 160iterations 1.7730187E-03 2.9737473E-02 at 170iterations 1.1187199E-03 2.0612717E-02 at 180iterations finished qdiffx linear iterations at : 11:33:47 total time elapsed so far: 14.32000 # loops : 180 mean,max change (kT/e) : 1.1187199E-03 2.0612717E-02 energy calculations done at 14.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.45000 DelPhi exited at 11:33:47 14.454u 0.243s 0:15.01 97.8% 0+0k 0+0io 0pf+0w