Tue Oct 11 03:19:51 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 03:19:51 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 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: 0.5407950 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 0.5407950 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3371 net assigned charge : -4.593971 assigned positive charge : 538.4550 centred at (gu) : 91.07271 92.09161 91.88457 assigned negative charge : -543.0508 centred at (gu) : 91.09132 92.10579 91.85760 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6689 nv = 96 ne = 84 npr = 70896 no. pairs analyzed = 70896 no. exposed pairs = 4577 no. arc points = 32207 no. surface atoms = 1510 nbur = 2006 mkacc time = 0.1200000 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 = 1.596000 m= 262 mr = 3409 m= 3 mr = 10 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 0.2500000 number of dielectric boundary points 3535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3293 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5801813E-10 -7.7987367E-11 midg,1,midg; midg,igrid,midg -8.4488083E-11 -5.4552368E-10 1,midg,midg; igrid,midg,midg -8.4656997E-11 -4.6125015E-10 gauss-seidel spectral radius is 0.9824160 estimated iterations to convergence 62 setup time was (sec) 0.4400000 now iterating at: 03:19:51 rms-change max change #iterations 7.8563660E-02 13.25150 at 10iterations 5.4359213E-03 0.9484081 at 20iterations 6.0564012E-04 9.3132973E-02 at 30iterations 1.4377029E-04 2.0946503E-02 at 40iterations 4.0927869E-05 5.4240227E-03 at 50iterations finished qdiffx linear iterations at : 03:19:54 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.0927869E-05 5.4240227E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:19:55 3.442u 0.171s 0:03.96 91.1% 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 03:19:55 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 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: 1.622385 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 1.622385 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3371 net assigned charge : -4.593971 assigned positive charge : 538.4550 centred at (gu) : 93.21763 96.27354 95.65287 assigned negative charge : -543.0508 centred at (gu) : 93.27348 96.31698 95.57237 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 74266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32207 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22805 mr = 50178 m= 2253 mr = 15334 m= 63 mr = 1005 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.3800000 number of dielectric boundary points 32868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 441 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25768 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) : 0.5407950 object centre at (A) : 19.49300 105.2545 133.2580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3388209E-03 4.2198189E-03 midg,1,midg; midg,igrid,midg 2.7478147E-02 -1.6663959E-02 1,midg,midg; igrid,midg,midg 7.7936109E-03 -3.2750329E-03 gauss-seidel spectral radius is 0.9982129 estimated iterations to convergence 188 setup time was (sec) 0.6000000 now iterating at: 03:19:55 rms-change max change #iterations 3.649094 152.2714 at 10iterations 1.525180 81.57361 at 20iterations 0.6391437 25.29187 at 30iterations 0.2676214 9.768427 at 40iterations 0.1123154 3.898999 at 50iterations 4.7129240E-02 1.523918 at 60iterations 1.9810770E-02 0.7065468 at 70iterations 8.4080258E-03 0.2875214 at 80iterations 3.5621754E-03 0.1175966 at 90iterations 1.5395473E-03 5.1219940E-02 at 100iterations 6.8096770E-04 2.2863865E-02 at 110iterations 3.1588675E-04 1.1284828E-02 at 120iterations finished qdiffx linear iterations at : 03:20:02 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 3.1588675E-04 1.1284828E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:20:03 7.796u 0.188s 0:08.29 96.1% 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 03:20:03 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 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: 2.433578 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 2.433578 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3371 net assigned charge : -4.593971 assigned positive charge : 538.4550 centred at (gu) : 94.82606 99.40993 98.47899 assigned negative charge : -543.0508 centred at (gu) : 94.91016 99.47519 98.35850 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32207 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 79468 mr = 123352 m= 21860 mr = 61997 m= 3346 mr = 16037 m= 215 mr = 2027 m= 6 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.9000000 number of dielectric boundary points 74126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 26926 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) : 1.622385 object centre at (A) : 19.49300 105.2545 133.2580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1960088E-02 9.8653838E-02 midg,1,midg; midg,igrid,midg 0.6017666 -0.4034200 1,midg,midg; igrid,midg,midg 0.1210837 -3.6155190E-02 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.130000 now iterating at: 03:20:04 rms-change max change #iterations 9.602705 352.5475 at 10iterations 5.475858 141.8079 at 20iterations 3.099028 78.04466 at 30iterations 1.742702 38.59963 at 40iterations 0.9764809 25.73962 at 50iterations 0.5468603 13.36063 at 60iterations 0.3051638 7.382071 at 70iterations 0.1698818 3.553728 at 80iterations 9.4713360E-02 2.026431 at 90iterations 5.2649636E-02 1.067127 at 100iterations 2.9215798E-02 0.6343231 at 110iterations 1.6244905E-02 0.3252835 at 120iterations 9.0332441E-03 0.1989784 at 130iterations 5.0298180E-03 0.1105957 at 140iterations 2.7965466E-03 5.7242870E-02 at 150iterations 1.5623606E-03 2.9546738E-02 at 160iterations 8.7854831E-04 1.7427921E-02 at 170iterations 4.9847405E-04 9.5423460E-03 at 180iterations finished qdiffx linear iterations at : 03:20:16 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 4.9847405E-04 9.5423460E-03 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 03:20:16 12.604u 0.210s 0:13.17 97.2% 0+0k 0+0io 0pf+0w