Tue Oct 11 07:54:27 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 07:54:27 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6434820 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 0.6434820 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2257 net assigned charge : 6.580012 assigned positive charge : 365.6303 centred at (gu) : 88.56510 90.20225 89.84740 assigned negative charge : -359.0507 centred at (gu) : 88.58877 90.14756 89.65005 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6699 nv = 96 ne = 84 npr = 48397 no. pairs analyzed = 48397 no. exposed pairs = 2891 no. arc points = 20246 no. surface atoms = 980 nbur = 1422 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 3785 m= 0 mr = 35 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1995 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7947 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3771483E-08 3.2367332E-08 midg,1,midg; midg,igrid,midg 3.9065342E-09 1.7741844E-08 1,midg,midg; igrid,midg,midg 1.8055250E-08 5.8279119E-09 gauss-seidel spectral radius is 0.9874676 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 07:54:28 rms-change max change #iterations 0.1470627 22.52037 at 10iterations 1.5458995E-02 2.130851 at 20iterations 1.7861743E-03 0.2690277 at 30iterations 2.5712649E-04 3.8391113E-02 at 40iterations 4.9300790E-05 7.5607300E-03 at 50iterations finished qdiffx linear iterations at : 07:54:30 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 4.9300790E-05 7.5607300E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 07:54:31 3.084u 0.155s 0:03.87 83.4% 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 Tue Oct 11 2011 at 07:54:31 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.930446 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 1.930446 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2257 net assigned charge : 6.580012 assigned positive charge : 365.6303 centred at (gu) : 85.69474 90.60635 89.54202 assigned negative charge : -359.0507 centred at (gu) : 85.76641 90.44248 88.95011 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20246 grid for indexing accessible points = 1.400000 m= 26989 mr = 50551 m= 4055 mr = 20203 m= 235 mr = 2453 m= 0 mr = 88 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5000000 number of dielectric boundary points 30049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17774 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) : 0.6434820 object centre at (A) : 26.16100 8.2499504E-02 31.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1276802E-02 4.4861708E-02 midg,1,midg; midg,igrid,midg -3.5725032E-05 5.4576569E-03 1,midg,midg; igrid,midg,midg 2.1405991E-02 2.5319241E-02 gauss-seidel spectral radius is 0.9986500 estimated iterations to convergence 216 setup time was (sec) 0.7700000 now iterating at: 07:54:32 rms-change max change #iterations 4.230337 188.9424 at 10iterations 1.984947 72.37675 at 20iterations 0.9406806 29.97884 at 30iterations 0.4425279 14.24586 at 40iterations 0.2094632 7.047522 at 50iterations 9.8473787E-02 3.450197 at 60iterations 4.6531525E-02 1.414574 at 70iterations 2.1920376E-02 0.7104950 at 80iterations 1.0443110E-02 0.3544540 at 90iterations 4.9563386E-03 0.1634254 at 100iterations 2.3772581E-03 8.3824158E-02 at 110iterations 1.1479313E-03 3.9871216E-02 at 120iterations finished qdiffx linear iterations at : 07:54:38 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 1.1479313E-03 3.9871216E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 07:54:38 6.872u 0.154s 0:07.34 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 Tue Oct 11 2011 at 07:54:38 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.895669 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 2.895669 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2257 net assigned charge : 6.580012 assigned positive charge : 365.6303 centred at (gu) : 83.54198 90.90952 89.31284 assigned negative charge : -359.0507 centred at (gu) : 83.64962 90.66355 88.42506 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20246 grid for indexing accessible points = 1.400000 m= 87307 mr = 121979 m= 31782 mr = 72271 m= 7114 mr = 25632 m= 977 mr = 5147 m= 56 mr = 661 m= 0 mr = 36 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 1032 time to turn everything in is 1.270000 number of dielectric boundary points 67907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18050 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) : 1.930446 object centre at (A) : 26.16100 8.2499504E-02 31.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2964480 0.4469512 midg,1,midg; midg,igrid,midg -2.6073921E-02 -5.0623037E-02 1,midg,midg; igrid,midg,midg 6.2295534E-02 0.1732073 gauss-seidel spectral radius is 0.9992541 estimated iterations to convergence 289 setup time was (sec) 1.540000 now iterating at: 07:54:40 rms-change max change #iterations 9.817018 405.6803 at 10iterations 5.728175 134.5319 at 20iterations 3.331586 77.73708 at 30iterations 1.925056 47.25981 at 40iterations 1.114526 25.42079 at 50iterations 0.6419456 14.48719 at 60iterations 0.3705921 6.549644 at 70iterations 0.2127741 4.347327 at 80iterations 0.1226835 2.370674 at 90iterations 7.0418775E-02 1.449135 at 100iterations 4.0418554E-02 0.7291145 at 110iterations 2.3264399E-02 0.4306903 at 120iterations 1.3381035E-02 0.2545184 at 130iterations 7.7181477E-03 0.1421680 at 140iterations 4.4628810E-03 8.3538055E-02 at 150iterations 2.5912239E-03 5.2284241E-02 at 160iterations 1.5249485E-03 3.1402290E-02 at 170iterations 9.1179204E-04 1.8051147E-02 at 180iterations finished qdiffx linear iterations at : 07:54:50 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 9.1179204E-04 1.8051147E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 07:54:50 11.303u 0.187s 0:12.05 95.2% 0+0k 0+0io 0pf+0w