Sat Oct 8 11:38:05 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 Sat Oct 8 2011 at 11:38:05 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5448090 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 0.5448090 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4707 net assigned charge : -6.5946519E-02 assigned positive charge : 733.8702 centred at (gu) : 90.34779 90.20494 90.59499 assigned negative charge : -733.9403 centred at (gu) : 90.24589 90.23417 90.66193 start vw surface at 0.2500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9036 nv = 96 ne = 84 npr = 101820 no. pairs analyzed = 101820 no. exposed pairs = 5784 no. arc points = 39969 no. surface atoms = 1953 nbur = 2923 mkacc time = 0.3000000 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 = 1.568000 m= 367 mr = 4894 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4098 ## 503 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 12220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9862354E-10 -8.2685037E-10 midg,1,midg; midg,igrid,midg 2.8853087E-10 -3.2662875E-10 1,midg,midg; igrid,midg,midg -9.9502817E-10 1.1515173E-09 gauss-seidel spectral radius is 0.9827650 estimated iterations to convergence 63 setup time was (sec) 0.9000000 now iterating at: 11:38:06 rms-change max change #iterations 9.3142807E-02 11.55299 at 10iterations 8.1641693E-03 1.521706 at 20iterations 1.6435822E-03 0.3525467 at 30iterations 4.8100966E-04 9.8098755E-02 at 40iterations 1.5499820E-04 2.8678894E-02 at 50iterations finished qdiffx linear iterations at : 11:38:09 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.5499820E-04 2.8678894E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:38:09 4.323u 0.214s 0:04.88 92.8% 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 Sat Oct 8 2011 at 11:38:10 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.634427 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 1.634427 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4707 net assigned charge : -6.5946519E-02 assigned positive charge : 733.8702 centred at (gu) : 91.04200 90.61347 91.78348 assigned negative charge : -733.9403 centred at (gu) : 90.73725 90.70205 91.98535 start vw surface at 0.2600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 101883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39969 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31987 mr = 71961 m= 3347 mr = 22001 m= 79 mr = 1669 m= 0 mr = 6 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 317 time to turn everything in is 0.9100000 number of dielectric boundary points 41659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 36014 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) : 0.5448090 object centre at (A) : 40.37900 35.34250 41.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6313147E-02 -1.5184283E-03 midg,1,midg; midg,igrid,midg -6.3334708E-03 -7.2413445E-03 1,midg,midg; igrid,midg,midg -1.2377787E-02 9.6882898E-03 gauss-seidel spectral radius is 0.9983752 estimated iterations to convergence 197 setup time was (sec) 1.240000 now iterating at: 11:38:11 rms-change max change #iterations 4.450073 225.7998 at 10iterations 1.940987 58.44163 at 20iterations 0.8516198 23.88358 at 30iterations 0.3728577 10.43559 at 40iterations 0.1634257 4.569344 at 50iterations 7.1762368E-02 2.080627 at 60iterations 3.1793989E-02 0.9178886 at 70iterations 1.4114211E-02 0.4109917 at 80iterations 6.4245290E-03 0.2153625 at 90iterations 3.0155149E-03 0.1061668 at 100iterations 1.4817488E-03 5.1490784E-02 at 110iterations 8.0272282E-04 2.9548645E-02 at 120iterations finished qdiffx linear iterations at : 11:38:19 total time elapsed so far: 8.970000 # loops : 120 mean,max change (kT/e) : 8.0272282E-04 2.9548645E-02 energy calculations done at 8.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 11:38:19 9.240u 0.210s 0:09.78 96.6% 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 Sat Oct 8 2011 at 11:38:19 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 470 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.451641 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): 7.707000 73.05099 ymin,ymax (A): 4.522000 66.16300 zmin,zma (A): 9.438999 74.52500 x,y,z range (A): 65.34399 61.64100 65.08600 scale (grids/A): 2.451641 object centre (A): 40.37900 35.34250 41.98200 number of atom coordinates read : 4876 total number of charged atoms : 4707 net assigned charge : -6.5946519E-02 assigned positive charge : 733.8702 centred at (gu) : 91.56275 90.91987 92.67489 assigned negative charge : -733.9403 centred at (gu) : 91.10574 91.05300 92.97794 start vw surface at 0.2600000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 237374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39969 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 110326 mr = 175886 m= 31852 mr = 87680 m= 5078 mr = 24040 m= 337 mr = 3301 m= 6 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 1010 time to turn everything in is 2.200000 number of dielectric boundary points 93940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 37618 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) : 1.634427 object centre at (A) : 40.37900 35.34250 41.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3769017 -0.2253281 midg,1,midg; midg,igrid,midg -0.1007510 -0.1489747 1,midg,midg; igrid,midg,midg -0.3357226 -7.5914976E-03 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 2.570000 now iterating at: 11:38:22 rms-change max change #iterations 11.56525 305.7424 at 10iterations 6.850217 150.0671 at 20iterations 4.038855 84.12768 at 30iterations 2.361303 47.41502 at 40iterations 1.375450 25.58189 at 50iterations 0.7989600 15.41889 at 60iterations 0.4631390 8.404128 at 70iterations 0.2679154 4.487976 at 80iterations 0.1546598 2.683907 at 90iterations 8.9510880E-02 1.645389 at 100iterations 5.1609423E-02 0.8683643 at 110iterations 2.9694729E-02 0.5401688 at 120iterations 1.7178671E-02 0.3129678 at 130iterations 9.9785477E-03 0.1798477 at 140iterations 5.8325976E-03 0.1034698 at 150iterations 3.4585418E-03 6.1264038E-02 at 160iterations 2.0972944E-03 4.2610168E-02 at 170iterations 1.3183696E-03 2.6130676E-02 at 180iterations finished qdiffx linear iterations at : 11:38:36 total time elapsed so far: 15.98000 # loops : 180 mean,max change (kT/e) : 1.3183696E-03 2.6130676E-02 energy calculations done at 15.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.22000 DelPhi exited at 11:38:36 16.219u 0.209s 0:16.91 97.0% 0+0k 0+0io 0pf+0w