Sat Oct 8 20:46:28 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 Sat Oct 8 2011 at 20:46:28 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 has a net charge of 1.4000 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: 0.6169309 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 0.6169309 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2416 net assigned charge : 3.406008 assigned positive charge : 386.3032 centred at (gu) : 88.54213 89.07331 89.51035 assigned negative charge : -382.8976 centred at (gu) : 88.44873 89.10119 89.40001 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6360 nv = 96 ne = 84 npr = 52813 no. pairs analyzed = 52813 no. exposed pairs = 2966 no. arc points = 21228 no. surface atoms = 998 nbur = 1557 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3589 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.3900000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5642370E-09 8.1784162E-09 midg,1,midg; midg,igrid,midg 5.2289240E-09 7.8059514E-10 1,midg,midg; igrid,midg,midg -4.2910284E-09 5.8974088E-09 gauss-seidel spectral radius is 0.9863883 estimated iterations to convergence 70 setup time was (sec) 0.7000000 now iterating at: 20:46:29 rms-change max change #iterations 0.1207915 23.55524 at 10iterations 1.1207701E-02 1.724504 at 20iterations 1.0407777E-03 0.1637516 at 30iterations 1.0432087E-04 1.5650749E-02 at 40iterations 1.0929210E-05 1.6784668E-03 at 50iterations finished qdiffx linear iterations at : 20:46:33 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 1.0929210E-05 1.6784668E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 20:46:33 4.468u 0.432s 0:05.15 94.9% 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 20:46:33 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 has a net charge of 1.4000 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: 1.850793 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 1.850793 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2416 net assigned charge : 3.406008 assigned positive charge : 386.3032 centred at (gu) : 85.62632 87.21944 88.53057 assigned negative charge : -382.8976 centred at (gu) : 85.34599 87.30325 88.19979 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 69794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 24208 mr = 49044 m= 3353 mr = 17882 m= 151 mr = 2000 m= 0 mr = 48 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3388 time to turn everything in is 0.7300000 number of dielectric boundary points 28532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 18936 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) : 0.6169309 object centre at (A) : -7.008000 2.4499893E-02 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7985461E-02 2.2302652E-02 midg,1,midg; midg,igrid,midg 1.2086781E-02 1.4747161E-03 1,midg,midg; igrid,midg,midg -3.2609047E-03 2.9107086E-02 gauss-seidel spectral radius is 0.9985499 estimated iterations to convergence 208 setup time was (sec) 1.050000 now iterating at: 20:46:35 rms-change max change #iterations 3.963003 175.7331 at 10iterations 1.817795 60.51627 at 20iterations 0.8301768 29.72250 at 30iterations 0.3810824 12.99962 at 40iterations 0.1747221 6.271877 at 50iterations 8.0359697E-02 2.664469 at 60iterations 3.6701836E-02 1.183374 at 70iterations 1.6811837E-02 0.5931454 at 80iterations 7.6721138E-03 0.2486477 at 90iterations 3.5283959E-03 0.1235924 at 100iterations 1.6169091E-03 5.8398962E-02 at 110iterations 7.4298464E-04 2.6060104E-02 at 120iterations finished qdiffx linear iterations at : 20:46:44 total time elapsed so far: 10.14000 # loops : 120 mean,max change (kT/e) : 7.4298464E-04 2.6060104E-02 energy calculations done at 10.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.35000 DelPhi exited at 20:46:44 10.358u 0.463s 0:11.10 97.3% 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 Sat Oct 8 2011 at 20:46:44 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 has a net charge of 1.4000 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: 2.776189 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 2.776189 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2416 net assigned charge : 3.406008 assigned positive charge : 386.3032 centred at (gu) : 83.43920 85.82900 87.79590 assigned negative charge : -382.8976 centred at (gu) : 83.01895 85.95473 87.29952 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 161503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 80516 mr = 118611 m= 26827 mr = 66329 m= 5772 mr = 21321 m= 642 mr = 4236 m= 21 mr = 393 m= 0 mr = 7 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 11883 time to turn everything in is 1.810000 number of dielectric boundary points 64384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 19327 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) : 1.850793 object centre at (A) : -7.008000 2.4499893E-02 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3072218E-02 0.2816181 midg,1,midg; midg,igrid,midg 0.1448510 -2.3321568E-03 1,midg,midg; igrid,midg,midg -3.8254067E-02 0.3910280 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 2.160000 now iterating at: 20:46:47 rms-change max change #iterations 9.334903 320.9865 at 10iterations 5.358269 108.1242 at 20iterations 3.056176 67.04111 at 30iterations 1.738700 34.47883 at 40iterations 0.9914087 19.84845 at 50iterations 0.5629147 10.83999 at 60iterations 0.3205238 5.986687 at 70iterations 0.1819873 3.286832 at 80iterations 0.1032606 2.008965 at 90iterations 5.8629144E-02 1.084091 at 100iterations 3.3289026E-02 0.5982943 at 110iterations 1.8959917E-02 0.3828239 at 120iterations 1.0739583E-02 0.1975069 at 130iterations 6.1005489E-03 0.1180210 at 140iterations 3.4670867E-03 6.7605972E-02 at 150iterations 1.9738469E-03 3.6945343E-02 at 160iterations 1.1222464E-03 2.2628784E-02 at 170iterations 6.4377242E-04 1.1992216E-02 at 180iterations finished qdiffx linear iterations at : 20:47:02 total time elapsed so far: 17.00000 # loops : 180 mean,max change (kT/e) : 6.4377242E-04 1.1992216E-02 energy calculations done at 17.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.22000 DelPhi exited at 20:47:02 17.223u 0.467s 0:18.01 98.1% 0+0k 0+0io 0pf+0w