Tue Oct 11 04:00:11 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 04:00:11 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6431797 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 0.6431797 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.154010 assigned positive charge : 415.0299 centred at (gu) : 89.94616 90.20061 91.74788 assigned negative charge : -413.8763 centred at (gu) : 89.68846 90.03983 91.68592 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7439 nv = 96 ne = 84 npr = 56516 no. pairs analyzed = 56516 no. exposed pairs = 3224 no. arc points = 22854 no. surface atoms = 1093 nbur = 1644 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4226 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5879469E-09 1.4676812E-08 midg,1,midg; midg,igrid,midg -1.9534742E-08 2.4102329E-08 1,midg,midg; igrid,midg,midg -3.4528238E-08 3.5188055E-08 gauss-seidel spectral radius is 0.9874825 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 04:00:12 rms-change max change #iterations 0.1571294 25.34899 at 10iterations 1.6000275E-02 2.106080 at 20iterations 1.7303183E-03 0.2186394 at 30iterations 2.2111913E-04 3.2402039E-02 at 40iterations 4.4311339E-05 5.8670044E-03 at 50iterations finished qdiffx linear iterations at : 04:00:15 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.4311339E-05 5.8670044E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 04:00:16 4.119u 0.246s 0:04.84 89.8% 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 04:00:16 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.929539 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 1.929539 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.154010 assigned positive charge : 415.0299 centred at (gu) : 89.83788 90.60139 95.24300 assigned negative charge : -413.8763 centred at (gu) : 89.06532 90.11936 95.05722 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22854 grid for indexing accessible points = 1.400000 m= 29590 mr = 56956 m= 4671 mr = 22153 m= 273 mr = 2895 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 864 time to turn everything in is 0.7100000 number of dielectric boundary points 33057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20339 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) : 0.6431797 object centre at (A) : 13.09700 -1.629000 17.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3776134E-02 -8.8879938E-04 midg,1,midg; midg,igrid,midg -1.3344076E-02 3.0342314E-02 1,midg,midg; igrid,midg,midg -1.7397011E-02 5.7038635E-02 gauss-seidel spectral radius is 0.9986801 estimated iterations to convergence 218 setup time was (sec) 1.020000 now iterating at: 04:00:17 rms-change max change #iterations 4.525263 224.8687 at 10iterations 2.145288 69.81757 at 20iterations 1.020379 34.69250 at 30iterations 0.4862506 14.34502 at 40iterations 0.2311051 7.359108 at 50iterations 0.1094558 3.218975 at 60iterations 5.2110072E-02 1.590194 at 70iterations 2.4702510E-02 0.7481289 at 80iterations 1.1761346E-02 0.3970222 at 90iterations 5.6052096E-03 0.1614840 at 100iterations 2.6634990E-03 7.9359055E-02 at 110iterations 1.2681480E-03 3.6384583E-02 at 120iterations finished qdiffx linear iterations at : 04:00:26 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 1.2681480E-03 3.6384583E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 04:00:26 9.548u 0.300s 0:10.12 97.2% 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 04:00:26 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.894309 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 2.894309 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.154010 assigned positive charge : 415.0299 centred at (gu) : 89.75679 90.90186 97.86423 assigned negative charge : -413.8763 centred at (gu) : 88.59787 90.17901 97.58566 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 186810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22854 grid for indexing accessible points = 1.400000 m= 95842 mr = 138079 m= 34808 mr = 79088 m= 8467 mr = 28184 m= 1238 mr = 6369 m= 80 mr = 837 m= 0 mr = 26 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 2950 time to turn everything in is 1.840000 number of dielectric boundary points 74662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 20674 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) : 1.929539 object centre at (A) : 13.09700 -1.629000 17.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8521600 0.2111810 midg,1,midg; midg,igrid,midg -0.1578446 0.3675303 1,midg,midg; igrid,midg,midg -0.1026298 0.5316045 gauss-seidel spectral radius is 0.9992673 estimated iterations to convergence 292 setup time was (sec) 2.170000 now iterating at: 04:00:29 rms-change max change #iterations 10.55018 437.2478 at 10iterations 6.176734 147.7209 at 20iterations 3.606994 81.01227 at 30iterations 2.100013 44.53598 at 40iterations 1.218551 29.13387 at 50iterations 0.7068049 13.19328 at 60iterations 0.4101732 7.275009 at 70iterations 0.2379263 4.258934 at 80iterations 0.1375636 2.486294 at 90iterations 7.9564445E-02 1.485291 at 100iterations 4.6030324E-02 0.7963066 at 110iterations 2.6667362E-02 0.4791737 at 120iterations 1.5457114E-02 0.2634640 at 130iterations 8.9835459E-03 0.1647339 at 140iterations 5.2541620E-03 0.1005573 at 150iterations 3.1049331E-03 5.4853857E-02 at 160iterations 1.8586610E-03 3.4532547E-02 at 170iterations 1.1423420E-03 2.1305084E-02 at 180iterations finished qdiffx linear iterations at : 04:00:43 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 1.1423420E-03 2.1305084E-02 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 04:00:43 16.139u 0.321s 0:16.78 98.0% 0+0k 0+0io 0pf+0w