Sun Oct 9 22:11:15 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 Sun Oct 9 2011 at 22:11:16 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: SEP 139 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: 0.5850068 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 0.5850068 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3030 net assigned charge : 5.025011 assigned positive charge : 484.5367 centred at (gu) : 91.91746 90.94514 89.61252 assigned negative charge : -479.5131 centred at (gu) : 91.96786 90.99362 89.62476 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7040 nv = 96 ne = 84 npr = 58991 no. pairs analyzed = 58991 no. exposed pairs = 4297 no. arc points = 30754 no. surface atoms = 1426 nbur = 1677 mkacc time = 0.1300000 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 = 1.456000 m= 323 mr = 3472 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3100000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8373247E-09 9.1852009E-10 midg,1,midg; midg,igrid,midg 2.1604627E-09 -3.7957505E-11 1,midg,midg; igrid,midg,midg 1.7664535E-09 -1.5782613E-10 gauss-seidel spectral radius is 0.9849352 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 22:11:16 rms-change max change #iterations 0.1033165 16.23923 at 10iterations 8.1278654E-03 1.563461 at 20iterations 6.5326993E-04 0.1119080 at 30iterations 5.2727937E-05 8.0275536E-03 at 40iterations 4.2821921E-06 6.2704086E-04 at 50iterations finished qdiffx linear iterations at : 22:11:19 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 4.2821921E-06 6.2704086E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 22:11:19 3.286u 0.232s 0:03.91 89.7% 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 Sun Oct 9 2011 at 22:11:20 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: SEP 139 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: 1.755020 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 1.755020 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3030 net assigned charge : 5.025011 assigned positive charge : 484.5367 centred at (gu) : 95.75155 92.83494 88.83675 assigned negative charge : -479.5131 centred at (gu) : 95.90347 92.98056 88.87353 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30754 grid for indexing accessible points = 1.400000 m= 24387 mr = 50264 m= 3046 mr = 16503 m= 121 mr = 1594 m= 0 mr = 16 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 36116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 23572 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) : 0.5850068 object centre at (A) : 6.146998 -9.734000 24.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9458723E-03 -1.2272855E-03 midg,1,midg; midg,igrid,midg -1.8783796E-03 2.5382920E-03 1,midg,midg; igrid,midg,midg -1.4360201E-02 4.4842674E-03 gauss-seidel spectral radius is 0.9984638 estimated iterations to convergence 202 setup time was (sec) 0.8100000 now iterating at: 22:11:21 rms-change max change #iterations 4.019211 164.7592 at 10iterations 1.777815 65.14398 at 20iterations 0.7910513 30.93996 at 30iterations 0.3532634 10.80058 at 40iterations 0.1573253 4.921349 at 50iterations 7.0285380E-02 2.466061 at 60iterations 3.1338163E-02 1.106373 at 70iterations 1.3930685E-02 0.4390392 at 80iterations 6.2521673E-03 0.2042789 at 90iterations 2.7805138E-03 0.1000023 at 100iterations 1.2437279E-03 4.4565201E-02 at 110iterations 5.5621908E-04 1.9020081E-02 at 120iterations finished qdiffx linear iterations at : 22:11:27 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 5.5621908E-04 1.9020081E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 22:11:27 7.091u 0.234s 0:07.79 93.9% 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 Sun Oct 9 2011 at 22:11:27 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 !!! WARNING: SEP 139 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: 2.632530 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): -24.28000 36.57400 ymin,ymax (A): -38.57700 19.10900 zmin,zma (A): -1.331000 51.14400 x,y,z range (A): 60.85400 57.68600 52.47500 scale (grids/A): 2.632530 object centre (A): 6.146998 -9.734000 24.90650 number of atom coordinates read : 3103 total number of charged atoms : 3030 net assigned charge : 5.025011 assigned positive charge : 484.5367 centred at (gu) : 98.62715 94.25223 88.25486 assigned negative charge : -479.5131 centred at (gu) : 98.85513 94.47086 88.31018 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 178514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30754 grid for indexing accessible points = 1.400000 m= 82077 mr = 123270 m= 25457 mr = 64073 m= 5025 mr = 18967 m= 466 mr = 3393 m= 11 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 81591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 24229 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) : 1.755020 object centre at (A) : 6.146998 -9.734000 24.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1317157 2.5163261E-02 midg,1,midg; midg,igrid,midg -4.3390663E-03 -0.1227606 1,midg,midg; igrid,midg,midg -0.3205783 1.9819371E-02 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.580000 now iterating at: 22:11:29 rms-change max change #iterations 10.09284 302.1171 at 10iterations 5.934783 138.0221 at 20iterations 3.458022 84.04697 at 30iterations 2.009888 45.81459 at 40iterations 1.158994 26.27649 at 50iterations 0.6691312 13.57617 at 60iterations 0.3843850 8.667900 at 70iterations 0.2204151 4.931210 at 80iterations 0.1264202 2.400997 at 90iterations 7.2302766E-02 1.391459 at 100iterations 4.1328292E-02 0.8177679 at 110iterations 2.3616830E-02 0.4281669 at 120iterations 1.3482107E-02 0.2729969 at 130iterations 7.6979855E-03 0.1628609 at 140iterations 4.3931147E-03 0.1017900 at 150iterations 2.5027802E-03 4.7800243E-02 at 160iterations 1.4264254E-03 2.5782228E-02 at 170iterations 8.1485638E-04 1.5221283E-02 at 180iterations finished qdiffx linear iterations at : 22:11:39 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 8.1485638E-04 1.5221283E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 22:11:40 11.925u 0.268s 0:12.56 96.9% 0+0k 0+0io 0pf+0w