Sun Oct 9 20:03:23 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 20:03:23 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5411239 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 0.5411239 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.6540542 assigned positive charge : 811.8107 centred at (gu) : 88.31386 89.10715 89.50299 assigned negative charge : -811.1626 centred at (gu) : 88.20691 89.11633 89.48122 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 10052 nv = 96 ne = 84 npr = 107005 no. pairs analyzed = 107005 no. exposed pairs = 6089 no. arc points = 41949 no. surface atoms = 2075 nbur = 3197 mkacc time = 0.2300000 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 = 1.596000 m= 402 mr = 5733 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4270 ## 538 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 13320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8718913E-10 2.4049127E-10 midg,1,midg; midg,igrid,midg 1.8375275E-10 -2.9959511E-11 1,midg,midg; igrid,midg,midg -1.5959611E-09 7.3007517E-10 gauss-seidel spectral radius is 0.9825607 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 20:03:24 rms-change max change #iterations 0.1033638 13.21142 at 10iterations 1.1646180E-02 1.540548 at 20iterations 4.5008645E-03 0.6510277 at 30iterations 2.1081686E-03 0.3187256 at 40iterations 9.9970249E-04 0.1537590 at 50iterations finished qdiffx linear iterations at : 20:03:27 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 9.9970249E-04 0.1537590 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 20:03:27 3.273u 0.139s 0:03.71 91.6% 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 Sun Oct 9 2011 at 20:03:27 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.623372 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 1.623372 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.6540542 assigned positive charge : 811.8107 centred at (gu) : 84.94053 87.32020 88.50751 assigned negative charge : -811.1626 centred at (gu) : 84.62038 87.34902 88.44357 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 113458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41949 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37954 mr = 82400 m= 4265 mr = 27379 m= 127 mr = 2215 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.7400000 number of dielectric boundary points 43790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 39052 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) : 0.5411239 object centre at (A) : 35.75600 22.32900 30.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4470742E-02 -6.7921816E-03 midg,1,midg; midg,igrid,midg 1.2536445E-02 8.8321315E-03 1,midg,midg; igrid,midg,midg -2.5987357E-02 6.1288108E-03 gauss-seidel spectral radius is 0.9983729 estimated iterations to convergence 197 setup time was (sec) 1.010000 now iterating at: 20:03:28 rms-change max change #iterations 4.713260 163.7120 at 10iterations 2.058320 61.19417 at 20iterations 0.9054708 25.10268 at 30iterations 0.3975554 11.52888 at 40iterations 0.1743804 5.399284 at 50iterations 7.7754982E-02 2.631702 at 60iterations 3.5516962E-02 1.028340 at 70iterations 1.7405588E-02 0.5803642 at 80iterations 9.6675567E-03 0.2955608 at 90iterations 6.1425464E-03 0.1947479 at 100iterations 4.2943470E-03 0.1303864 at 110iterations 3.1709634E-03 9.8789215E-02 at 120iterations finished qdiffx linear iterations at : 20:03:35 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 3.1709634E-03 9.8789215E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 20:03:35 7.539u 0.175s 0:07.99 96.3% 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 20:03:35 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.435057 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 2.435057 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.6540542 assigned positive charge : 811.8107 centred at (gu) : 82.41042 85.98000 87.76096 assigned negative charge : -811.1626 centred at (gu) : 81.93062 86.02362 87.66537 start vw surface at 0.2600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 264025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41949 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130856 mr = 200691 m= 39370 mr = 106783 m= 6713 mr = 30368 m= 558 mr = 4502 m= 10 mr = 306 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 1.860000 number of dielectric boundary points 98882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 40797 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) : 1.623372 object centre at (A) : 35.75600 22.32900 30.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3169372 -0.1970486 midg,1,midg; midg,igrid,midg 0.1302105 2.8025480E-02 1,midg,midg; igrid,midg,midg -0.4643793 5.4439515E-02 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 2.140000 now iterating at: 20:03:37 rms-change max change #iterations 12.02783 315.5179 at 10iterations 7.040804 138.9713 at 20iterations 4.086807 80.18560 at 30iterations 2.368458 43.57308 at 40iterations 1.365227 23.65494 at 50iterations 0.7870164 14.61352 at 60iterations 0.4526330 7.838103 at 70iterations 0.2594261 4.064442 at 80iterations 0.1488423 2.781708 at 90iterations 8.5876435E-02 1.462512 at 100iterations 4.9517486E-02 0.8051682 at 110iterations 2.8899480E-02 0.4965515 at 120iterations 1.7223457E-02 0.3385010 at 130iterations 1.0663524E-02 0.2077179 at 140iterations 6.9674361E-03 0.1370239 at 150iterations 4.8857536E-03 9.3738556E-02 at 160iterations 3.6710878E-03 7.2593689E-02 at 170iterations 2.9013979E-03 5.6022644E-02 at 180iterations finished qdiffx linear iterations at : 20:03:47 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 2.9013979E-03 5.6022644E-02 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 20:03:48 11.963u 0.187s 0:12.44 97.5% 0+0k 0+0io 0pf+0w