Mon Oct 10 16:04:02 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 16:04:02 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4732 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5485785 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 0.5485785 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4569 net assigned charge : 2.906006 assigned positive charge : 712.7208 centred at (gu) : 89.55173 89.91090 88.49559 assigned negative charge : -709.8190 centred at (gu) : 89.49784 89.86626 88.46510 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9140 nv = 96 ne = 84 npr = 97161 no. pairs analyzed = 97161 no. exposed pairs = 5824 no. arc points = 39256 no. surface atoms = 1960 nbur = 2772 mkacc time = 0.2100000 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 = 1.540000 m= 386 mr = 5004 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4075 ## 490 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12116 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2087689E-10 3.9028106E-10 midg,1,midg; midg,igrid,midg -3.2121339E-10 7.1123041E-10 1,midg,midg; igrid,midg,midg -4.7470522E-10 7.4612061E-10 gauss-seidel spectral radius is 0.9829920 estimated iterations to convergence 63 setup time was (sec) 0.6700000 now iterating at: 16:04:03 rms-change max change #iterations 9.9047408E-02 15.17744 at 10iterations 7.3851659E-03 1.204727 at 20iterations 1.2470561E-03 0.2016983 at 30iterations 4.7726370E-04 6.6806793E-02 at 40iterations 2.0689644E-04 2.4854660E-02 at 50iterations finished qdiffx linear iterations at : 16:04:06 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.0689644E-04 2.4854660E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:04:06 3.449u 0.182s 0:03.91 92.5% 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 16:04:06 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 = 4732 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.645736 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 1.645736 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4569 net assigned charge : 2.906006 assigned positive charge : 712.7208 centred at (gu) : 88.65325 89.73115 85.48526 assigned negative charge : -709.8190 centred at (gu) : 88.49283 89.59835 85.39491 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 101785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39256 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32745 mr = 72015 m= 3722 mr = 22947 m= 104 mr = 1871 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 0.7000000 number of dielectric boundary points 41518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 414 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 35091 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) : 0.5485785 object centre at (A) : 35.24950 2.516500 3.237499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0720749E-03 -5.7720840E-03 midg,1,midg; midg,igrid,midg 1.4181862E-02 1.2410875E-02 1,midg,midg; igrid,midg,midg -1.2626138E-03 4.6058698E-03 gauss-seidel spectral radius is 0.9983836 estimated iterations to convergence 197 setup time was (sec) 1.000000 now iterating at: 16:04:07 rms-change max change #iterations 4.421712 161.5396 at 10iterations 1.937730 58.06946 at 20iterations 0.8496243 24.95942 at 30iterations 0.3724058 11.98409 at 40iterations 0.1635200 4.464378 at 50iterations 7.1897410E-02 1.969359 at 60iterations 3.1643022E-02 0.9670982 at 70iterations 1.4027254E-02 0.4584942 at 80iterations 6.3313167E-03 0.1928291 at 90iterations 2.9493456E-03 0.1063786 at 100iterations 1.4674009E-03 4.8439026E-02 at 110iterations 8.3278120E-04 2.6203156E-02 at 120iterations finished qdiffx linear iterations at : 16:04:14 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 8.3278120E-04 2.6203156E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 16:04:14 7.760u 0.191s 0:08.25 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 Mon Oct 10 2011 at 16:04:14 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 = 4732 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.468603 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 2.468603 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4569 net assigned charge : 2.906006 assigned positive charge : 712.7208 centred at (gu) : 87.97954 89.59627 83.22759 assigned negative charge : -709.8190 centred at (gu) : 87.73924 89.39740 83.09220 start vw surface at 0.2400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 237095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39256 grid for indexing accessible points = 1.400000 m= 112403 mr = 176342 m= 33159 mr = 89732 m= 5907 mr = 25165 m= 490 mr = 3937 m= 17 mr = 202 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 3119 time to turn everything in is 1.740000 number of dielectric boundary points 93694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 36504 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) : 1.645736 object centre at (A) : 35.24950 2.516500 3.237499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1610792 -0.1284446 midg,1,midg; midg,igrid,midg 0.3139357 0.1154808 1,midg,midg; igrid,midg,midg 1.4551698E-02 8.1289463E-02 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 2.060000 now iterating at: 16:04:17 rms-change max change #iterations 11.46373 347.1486 at 10iterations 6.759789 160.8711 at 20iterations 3.954400 83.02463 at 30iterations 2.307001 45.57142 at 40iterations 1.339243 23.91918 at 50iterations 0.7746164 13.65820 at 60iterations 0.4462495 8.574095 at 70iterations 0.2576728 4.484354 at 80iterations 0.1482320 2.595096 at 90iterations 8.5084237E-02 1.625162 at 100iterations 4.8862446E-02 0.8507094 at 110iterations 2.8058024E-02 0.4550934 at 120iterations 1.6127486E-02 0.2838488 at 130iterations 9.2955781E-03 0.1683197 at 140iterations 5.3962306E-03 9.7015619E-02 at 150iterations 3.1711527E-03 5.8534622E-02 at 160iterations 1.9164989E-03 3.4149170E-02 at 170iterations 1.2091505E-03 2.0633698E-02 at 180iterations finished qdiffx linear iterations at : 16:04:27 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.2091505E-03 2.0633698E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 16:04:28 13.056u 0.207s 0:13.60 97.4% 0+0k 0+0io 0pf+0w