Sat Oct 8 18:39:58 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+sph.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 = amb.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 18:39:58 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2568 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6291086 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): -32.09500 17.64100 ymin,ymax (A): -23.84600 22.43800 zmin,zma (A): -12.08400 44.50400 x,y,z range (A): 49.73600 46.28400 56.58800 scale (grids/A): 0.6291086 object centre (A): -7.227000 -0.7039995 16.21000 number of atom coordinates read : 2568 total number of charged atoms : 2460 net assigned charge : 4.000004 assigned positive charge : 390.9750 centred at (gu) : 88.57514 89.48466 89.77239 assigned negative charge : -386.9755 centred at (gu) : 88.47354 89.52940 89.66910 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6743 nv = 96 ne = 84 npr = 52502 no. pairs analyzed = 52502 no. exposed pairs = 3038 no. arc points = 21751 no. surface atoms = 1019 nbur = 1549 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3804 m= 0 mr = 46 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.2000000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2126 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8287 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8359765E-09 1.2504514E-08 midg,1,midg; midg,igrid,midg 9.1634265E-09 4.8755289E-10 1,midg,midg; igrid,midg,midg -6.2040040E-09 9.5557953E-09 gauss-seidel spectral radius is 0.9869080 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 18:39:59 rms-change max change #iterations 0.1368492 22.27982 at 10iterations 1.2852791E-02 1.941792 at 20iterations 1.2236951E-03 0.2046014 at 30iterations 1.1620020E-04 1.7723083E-02 at 40iterations 1.1169343E-05 1.8110275E-03 at 50iterations finished qdiffx linear iterations at : 18:40:02 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.1169343E-05 1.8110275E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 18:40:02 3.560u 0.189s 0:04.03 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 18:40:02 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2568 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.887326 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): -32.09500 17.64100 ymin,ymax (A): -23.84600 22.43800 zmin,zma (A): -12.08400 44.50400 x,y,z range (A): 49.73600 46.28400 56.58800 scale (grids/A): 1.887326 object centre (A): -7.227000 -0.7039995 16.21000 number of atom coordinates read : 2568 total number of charged atoms : 2460 net assigned charge : 4.000004 assigned positive charge : 390.9750 centred at (gu) : 85.72491 88.45352 89.31662 assigned negative charge : -386.9755 centred at (gu) : 85.42024 88.58787 89.00705 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21751 grid for indexing accessible points = 1.400000 m= 26788 mr = 51573 m= 4082 mr = 20253 m= 255 mr = 2622 m= 0 mr = 109 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 6734 time to turn everything in is 0.3700000 number of dielectric boundary points 29983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19333 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) : 0.6291086 object centre at (A) : -7.227000 -0.7039995 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9300733E-02 2.6900019E-02 midg,1,midg; midg,igrid,midg 1.3735425E-02 3.9656990E-04 1,midg,midg; igrid,midg,midg -3.6677618E-03 4.0155083E-02 gauss-seidel spectral radius is 0.9986073 estimated iterations to convergence 212 setup time was (sec) 0.6000000 now iterating at: 18:40:03 rms-change max change #iterations 4.149630 192.4083 at 10iterations 1.926546 73.59502 at 20iterations 0.8929857 30.44724 at 30iterations 0.4153776 14.84453 at 40iterations 0.1931707 6.200726 at 50iterations 8.9967892E-02 2.804733 at 60iterations 4.1764807E-02 1.306528 at 70iterations 1.9387862E-02 0.6244220 at 80iterations 9.0313079E-03 0.3067780 at 90iterations 4.2148875E-03 0.1386175 at 100iterations 1.9569891E-03 5.9056282E-02 at 110iterations 9.1035833E-04 2.9057980E-02 at 120iterations finished qdiffx linear iterations at : 18:40:10 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 9.1035833E-04 2.9057980E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 18:40:11 8.208u 0.227s 0:08.75 96.2% 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 Sat Oct 8 2011 at 18:40:11 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2568 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.830989 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): -32.09500 17.64100 ymin,ymax (A): -23.84600 22.43800 zmin,zma (A): -12.08400 44.50400 x,y,z range (A): 49.73600 46.28400 56.58800 scale (grids/A): 2.830989 object centre (A): -7.227000 -0.7039995 16.21000 number of atom coordinates read : 2568 total number of charged atoms : 2460 net assigned charge : 4.000004 assigned positive charge : 390.9750 centred at (gu) : 83.58743 87.68022 88.97479 assigned negative charge : -386.9755 centred at (gu) : 83.13039 87.88178 88.51057 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21751 grid for indexing accessible points = 1.400000 m= 87379 mr = 124417 m= 31216 mr = 72681 m= 7137 mr = 25488 m= 1046 mr = 5473 m= 66 mr = 772 m= 0 mr = 24 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 22752 time to turn everything in is 0.9400000 number of dielectric boundary points 67689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 19678 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) : 1.887326 object centre at (A) : -7.227000 -0.7039995 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1216651 0.3507997 midg,1,midg; midg,igrid,midg 0.1600317 -1.2052160E-02 1,midg,midg; igrid,midg,midg 7.1261078E-03 0.4984832 gauss-seidel spectral radius is 0.9992457 estimated iterations to convergence 287 setup time was (sec) 1.200000 now iterating at: 18:40:12 rms-change max change #iterations 9.620989 307.0808 at 10iterations 5.559337 125.4212 at 20iterations 3.176496 66.82793 at 30iterations 1.821999 41.37037 at 40iterations 1.044322 22.88017 at 50iterations 0.5968636 11.48880 at 60iterations 0.3422641 7.581697 at 70iterations 0.1947742 3.630976 at 80iterations 0.1118612 2.345638 at 90iterations 6.3749351E-02 1.213007 at 100iterations 3.6408760E-02 0.6832218 at 110iterations 2.0773783E-02 0.3914776 at 120iterations 1.1905529E-02 0.2230721 at 130iterations 6.7909551E-03 0.1298923 at 140iterations 3.8775441E-03 7.4686050E-02 at 150iterations 2.2171428E-03 4.0266037E-02 at 160iterations 1.2624229E-03 2.2232056E-02 at 170iterations 7.2372821E-04 1.3413429E-02 at 180iterations finished qdiffx linear iterations at : 18:40:25 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 7.2372821E-04 1.3413429E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 18:40:25 13.774u 0.253s 0:14.43 97.1% 0+0k 0+0io 0pf+0w