Mon Oct 10 09:44:33 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 Mon Oct 10 2011 at 09:44:33 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2921 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5412967 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 0.5412967 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 6.914017 assigned positive charge : 431.2418 centred at (gu) : 88.47936 89.48767 86.87259 assigned negative charge : -424.3283 centred at (gu) : 88.32061 89.40619 86.70042 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5704 nv = 96 ne = 84 npr = 56688 no. pairs analyzed = 56688 no. exposed pairs = 4305 no. arc points = 31443 no. surface atoms = 1435 nbur = 1486 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 = 1.568000 m= 244 mr = 2473 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3154 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1895109E-09 5.9416050E-10 midg,1,midg; midg,igrid,midg -3.3508012E-11 7.2471457E-10 1,midg,midg; igrid,midg,midg -6.6335815E-10 8.3272439E-10 gauss-seidel spectral radius is 0.9824203 estimated iterations to convergence 62 setup time was (sec) 0.5900000 now iterating at: 09:44:34 rms-change max change #iterations 7.0353448E-02 13.59756 at 10iterations 4.5196335E-03 0.8854465 at 20iterations 3.0202413E-04 5.6911767E-02 at 30iterations 2.4530817E-05 3.6625862E-03 at 40iterations 3.5031312E-06 4.3010712E-04 at 50iterations finished qdiffx linear iterations at : 09:44:37 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.5031312E-06 4.3010712E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 09:44:37 3.616u 0.187s 0:04.11 92.2% 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 Mon Oct 10 2011 at 09:44:37 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2921 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.623890 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 1.623890 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 6.914017 assigned positive charge : 431.2418 centred at (gu) : 85.43760 88.46247 80.61718 assigned negative charge : -424.3283 centred at (gu) : 84.96178 88.21847 80.10100 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18784 mr = 37742 m= 2041 mr = 11887 m= 74 mr = 828 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 32250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21206 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) : 0.5412967 object centre at (A) : -10.70500 137.4635 181.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7525905E-03 8.7750414E-03 midg,1,midg; midg,igrid,midg -3.1784286E-03 1.7041100E-02 1,midg,midg; igrid,midg,midg -1.6648114E-02 2.0202080E-02 gauss-seidel spectral radius is 0.9981713 estimated iterations to convergence 186 setup time was (sec) 0.8200000 now iterating at: 09:44:38 rms-change max change #iterations 3.202694 148.2195 at 10iterations 1.321398 55.89613 at 20iterations 0.5454463 21.00356 at 30iterations 0.2253444 8.683490 at 40iterations 9.3148313E-02 3.434097 at 50iterations 3.8518775E-02 1.457992 at 60iterations 1.6011218E-02 0.6473598 at 70iterations 6.6263820E-03 0.2423840 at 80iterations 2.7515825E-03 9.8901987E-02 at 90iterations 1.1378601E-03 4.5809269E-02 at 100iterations 4.7325762E-04 1.8991470E-02 at 110iterations 1.9681973E-04 7.1201324E-03 at 120iterations finished qdiffx linear iterations at : 09:44:45 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 1.9681973E-04 7.1201324E-03 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 09:44:46 8.205u 0.245s 0:08.73 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 Mon Oct 10 2011 at 09:44:46 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2921 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.435835 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 2.435835 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 6.914017 assigned positive charge : 431.2418 centred at (gu) : 83.15632 87.69347 75.92557 assigned negative charge : -424.3283 centred at (gu) : 82.44253 87.32754 75.15138 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63297 mr = 93332 m= 18941 mr = 47198 m= 3030 mr = 13372 m= 200 mr = 1673 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 72708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22127 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) : 1.623890 object centre at (A) : -10.70500 137.4635 181.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7894077E-02 0.1116349 midg,1,midg; midg,igrid,midg -0.1750479 0.3391052 1,midg,midg; igrid,midg,midg -0.5168750 0.6784754 gauss-seidel spectral radius is 0.9991386 estimated iterations to convergence 269 setup time was (sec) 1.510000 now iterating at: 09:44:48 rms-change max change #iterations 8.626075 364.0729 at 10iterations 4.931654 130.1746 at 20iterations 2.773847 83.78899 at 30iterations 1.555980 45.00508 at 40iterations 0.8698885 23.41476 at 50iterations 0.4851104 12.18218 at 60iterations 0.2685492 6.618122 at 70iterations 0.1489499 3.349670 at 80iterations 8.2002133E-02 2.044670 at 90iterations 4.5285385E-02 1.132039 at 100iterations 2.4993248E-02 0.5849686 at 110iterations 1.3778727E-02 0.3089117 at 120iterations 7.5716241E-03 0.1688013 at 130iterations 4.1728402E-03 0.1083353 at 140iterations 2.2941707E-03 5.2909851E-02 at 150iterations 1.2580258E-03 2.6250839E-02 at 160iterations 6.9458591E-04 1.4630318E-02 at 170iterations 3.8097255E-04 8.2406998E-03 at 180iterations finished qdiffx linear iterations at : 09:44:58 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 3.8097255E-04 8.2406998E-03 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 09:44:58 11.870u 0.246s 0:12.39 97.7% 0+0k 0+0io 0pf+0w