Sat Oct 8 11:46:33 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+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 11:46:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2465 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: 0.6323268 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): -24.97500 31.32500 ymin,ymax (A): -5.585000 39.53500 zmin,zma (A): 8.550000 50.89200 x,y,z range (A): 56.30000 45.12000 42.34200 scale (grids/A): 0.6323268 object centre (A): 3.174999 16.97500 29.72100 number of atom coordinates read : 2465 total number of charged atoms : 2325 net assigned charge : -2.999994 assigned positive charge : 373.2303 centred at (gu) : 89.84309 89.38163 91.01301 assigned negative charge : -376.2307 centred at (gu) : 89.94692 89.28992 90.99757 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6460 nv = 96 ne = 84 npr = 50916 no. pairs analyzed = 50916 no. exposed pairs = 2923 no. arc points = 21226 no. surface atoms = 979 nbur = 1486 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3537 m= 0 mr = 43 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3700000 number of dielectric boundary points 3208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2071 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7917 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9322843E-09 -2.5107592E-09 midg,1,midg; midg,igrid,midg -1.3646829E-08 4.2064054E-09 1,midg,midg; igrid,midg,midg 6.1449801E-09 -1.2619881E-08 gauss-seidel spectral radius is 0.9870307 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 11:46:34 rms-change max change #iterations 0.1350642 19.75340 at 10iterations 1.2753196E-02 1.686641 at 20iterations 1.2489611E-03 0.1844788 at 30iterations 1.1979457E-04 1.7980576E-02 at 40iterations 1.1546543E-05 1.7490387E-03 at 50iterations finished qdiffx linear iterations at : 11:46:37 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.1546543E-05 1.7490387E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 11:46:38 4.393u 0.454s 0:05.11 94.7% 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 Sat Oct 8 2011 at 11:46:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2465 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: 1.896981 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): -24.97500 31.32500 ymin,ymax (A): -5.585000 39.53500 zmin,zma (A): 8.550000 50.89200 x,y,z range (A): 56.30000 45.12000 42.34200 scale (grids/A): 1.896981 object centre (A): 3.174999 16.97500 29.72100 number of atom coordinates read : 2465 total number of charged atoms : 2325 net assigned charge : -2.999994 assigned positive charge : 373.2303 centred at (gu) : 89.52899 88.14427 93.03860 assigned negative charge : -376.2307 centred at (gu) : 89.84061 87.86954 92.99264 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 23822 mr = 48726 m= 3779 mr = 17307 m= 232 mr = 2288 m= 1 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 712 time to turn everything in is 0.7000000 number of dielectric boundary points 29730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 18273 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) : 0.6323268 object centre at (A) : 3.174999 16.97500 29.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9250550E-04 -1.4278753E-02 midg,1,midg; midg,igrid,midg -1.0013837E-02 -1.7920427E-04 1,midg,midg; igrid,midg,midg 1.1417521E-02 -4.4355083E-02 gauss-seidel spectral radius is 0.9986091 estimated iterations to convergence 213 setup time was (sec) 1.010000 now iterating at: 11:46:39 rms-change max change #iterations 4.104900 190.0087 at 10iterations 1.900622 75.73763 at 20iterations 0.8809119 27.81211 at 30iterations 0.4113053 14.16801 at 40iterations 0.1905434 6.320656 at 50iterations 8.8630132E-02 2.916902 at 60iterations 4.1357473E-02 1.525587 at 70iterations 1.9150011E-02 0.6172934 at 80iterations 8.9123016E-03 0.2803059 at 90iterations 4.1307467E-03 0.1504145 at 100iterations 1.9250487E-03 6.1816216E-02 at 110iterations 8.9454488E-04 2.7571678E-02 at 120iterations finished qdiffx linear iterations at : 11:46:48 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 8.9454488E-04 2.7571678E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 11:46:49 10.145u 0.507s 0:10.97 96.9% 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 Sat Oct 8 2011 at 11:46:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2465 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: 2.845471 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): -24.97500 31.32500 ymin,ymax (A): -5.585000 39.53500 zmin,zma (A): 8.550000 50.89200 x,y,z range (A): 56.30000 45.12000 42.34200 scale (grids/A): 2.845471 object centre (A): 3.174999 16.97500 29.72100 number of atom coordinates read : 2465 total number of charged atoms : 2325 net assigned charge : -2.999994 assigned positive charge : 373.2303 centred at (gu) : 89.29336 87.21635 94.55773 assigned negative charge : -376.2307 centred at (gu) : 89.76093 86.80425 94.48888 start vw surface at 0.1500000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 162974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 78488 mr = 118387 m= 27160 mr = 63812 m= 6533 mr = 21476 m= 965 mr = 4738 m= 45 mr = 654 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 2429 time to turn everything in is 1.820000 number of dielectric boundary points 67082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 18596 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) : 1.896981 object centre at (A) : 3.174999 16.97500 29.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7784104E-02 -0.2153366 midg,1,midg; midg,igrid,midg -0.1166306 -4.5464311E-02 1,midg,midg; igrid,midg,midg 0.2023275 -0.6247736 gauss-seidel spectral radius is 0.9992463 estimated iterations to convergence 287 setup time was (sec) 2.200000 now iterating at: 11:46:51 rms-change max change #iterations 9.607624 418.5692 at 10iterations 5.544236 122.0863 at 20iterations 3.177621 63.97102 at 30iterations 1.815041 33.17530 at 40iterations 1.040423 20.35061 at 50iterations 0.5925462 11.20734 at 60iterations 0.3383760 6.452309 at 70iterations 0.1930478 3.724632 at 80iterations 0.1104697 2.250434 at 90iterations 6.3083977E-02 1.102257 at 100iterations 3.6014985E-02 0.7191162 at 110iterations 2.0547345E-02 0.3963623 at 120iterations 1.1712085E-02 0.2122633 at 130iterations 6.6793715E-03 0.1212046 at 140iterations 3.8117953E-03 6.8864822E-02 at 150iterations 2.1764839E-03 4.2205811E-02 at 160iterations 1.2384767E-03 2.3559570E-02 at 170iterations 7.0793752E-04 1.3235092E-02 at 180iterations finished qdiffx linear iterations at : 11:47:06 total time elapsed so far: 16.95000 # loops : 180 mean,max change (kT/e) : 7.0793752E-04 1.3235092E-02 energy calculations done at 16.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.17000 DelPhi exited at 11:47:07 17.171u 0.501s 0:17.95 98.4% 0+0k 0+0io 0pf+0w