Mon Oct 10 14:02:06 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 Mon Oct 10 2011 at 14:02:06 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 0.6724848 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): -23.73000 24.33600 ymin,ymax (A): 7.692000 53.94000 zmin,zma (A): -20.63300 32.30500 x,y,z range (A): 48.06600 46.24800 52.93800 scale (grids/A): 0.6724848 object centre (A): 0.3030005 30.81600 5.835999 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -6.271979 assigned positive charge : 328.0037 centred at (gu) : 89.68665 89.69191 89.24911 assigned negative charge : -334.2759 centred at (gu) : 89.71249 89.61951 89.09505 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6751 nv = 96 ne = 84 npr = 42975 no. pairs analyzed = 42975 no. exposed pairs = 2852 no. arc points = 20427 no. surface atoms = 964 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3612 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1876 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7641 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8062505E-08 1.1400867E-08 midg,1,midg; midg,igrid,midg -4.1337007E-08 -4.8341073E-09 1,midg,midg; igrid,midg,midg -1.6801410E-08 -2.6184381E-08 gauss-seidel spectral radius is 0.9885051 estimated iterations to convergence 76 setup time was (sec) 0.5600000 now iterating at: 14:02:07 rms-change max change #iterations 0.1674564 24.47987 at 10iterations 1.8612273E-02 2.576546 at 20iterations 2.0594520E-03 0.3049870 at 30iterations 2.2604235E-04 3.5266876E-02 at 40iterations 2.4779536E-05 3.7403107E-03 at 50iterations finished qdiffx linear iterations at : 14:02:10 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.4779536E-05 3.7403107E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:02:11 3.664u 0.200s 0:04.75 81.2% 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 Mon Oct 10 2011 at 14:02:11 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 2.017454 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): -23.73000 24.33600 ymin,ymax (A): 7.692000 53.94000 zmin,zma (A): -20.63300 32.30500 x,y,z range (A): 48.06600 46.24800 52.93800 scale (grids/A): 2.017454 object centre (A): 0.3030005 30.81600 5.835999 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -6.271979 assigned positive charge : 328.0037 centred at (gu) : 89.05967 89.07539 87.74748 assigned negative charge : -334.2759 centred at (gu) : 89.13754 88.85846 87.28508 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20427 grid for indexing accessible points = 1.400000 m= 26321 mr = 48278 m= 4604 mr = 19372 m= 297 mr = 2954 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 32285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16055 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) : 0.6724848 object centre at (A) : 0.3030005 30.81600 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1548093E-02 1.5062104E-02 midg,1,midg; midg,igrid,midg -2.6879273E-02 -2.0150814E-02 1,midg,midg; igrid,midg,midg -7.4082101E-04 5.0123464E-03 gauss-seidel spectral radius is 0.9987436 estimated iterations to convergence 223 setup time was (sec) 0.8900000 now iterating at: 14:02:12 rms-change max change #iterations 4.375699 187.9442 at 10iterations 2.115725 81.98304 at 20iterations 1.015609 36.57373 at 30iterations 0.4888211 15.50108 at 40iterations 0.2359804 7.418924 at 50iterations 0.1137181 3.419173 at 60iterations 5.4818727E-02 1.762363 at 70iterations 2.6422122E-02 0.8152962 at 80iterations 1.2741256E-02 0.3683987 at 90iterations 6.1826939E-03 0.2324829 at 100iterations 2.9761111E-03 0.1020966 at 110iterations 1.4282410E-03 4.9251556E-02 at 120iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 1.4282410E-03 4.9251556E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 14:02:21 9.282u 0.224s 0:10.00 95.0% 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 Mon Oct 10 2011 at 14:02:21 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 3.026181 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): -23.73000 24.33600 ymin,ymax (A): 7.692000 53.94000 zmin,zma (A): -20.63300 32.30500 x,y,z range (A): 48.06600 46.24800 52.93800 scale (grids/A): 3.026181 object centre (A): 0.3030005 30.81600 5.835999 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -6.271979 assigned positive charge : 328.0037 centred at (gu) : 88.58956 88.61314 86.62120 assigned negative charge : -334.2759 centred at (gu) : 88.70625 88.28772 85.92751 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 165784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20427 grid for indexing accessible points = 1.400000 m= 83450 mr = 117522 m= 31718 mr = 67703 m= 8386 mr = 25489 m= 1362 mr = 6432 m= 105 mr = 926 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 72697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 16248 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) : 2.017454 object centre at (A) : 0.3030005 30.81600 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9714159 0.1268575 midg,1,midg; midg,igrid,midg -0.2044267 -0.2092324 1,midg,midg; igrid,midg,midg -2.4896111E-02 8.9647479E-02 gauss-seidel spectral radius is 0.9992787 estimated iterations to convergence 294 setup time was (sec) 1.780000 now iterating at: 14:02:23 rms-change max change #iterations 9.965226 430.4911 at 10iterations 5.779823 183.7570 at 20iterations 3.361320 70.89791 at 30iterations 1.938998 40.90242 at 40iterations 1.124082 22.32895 at 50iterations 0.6505153 11.60549 at 60iterations 0.3754157 6.643999 at 70iterations 0.2172055 3.940332 at 80iterations 0.1256538 2.269422 at 90iterations 7.2486103E-02 1.323709 at 100iterations 4.1970253E-02 0.8506136 at 110iterations 2.4246063E-02 0.5020614 at 120iterations 1.4011602E-02 0.2604370 at 130iterations 8.0723362E-03 0.1405602 at 140iterations 4.6680146E-03 8.8658810E-02 at 150iterations 2.6928089E-03 4.9039841E-02 at 160iterations 1.5574347E-03 2.6596069E-02 at 170iterations 9.0175943E-04 1.6733170E-02 at 180iterations finished qdiffx linear iterations at : 14:02:33 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 9.0175943E-04 1.6733170E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 14:02:34 12.420u 0.239s 0:13.38 94.5% 0+0k 0+0io 0pf+0w