Tue Oct 11 08:37:35 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 Tue Oct 11 2011 at 08:37:35 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2127 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 !!! WARNING: SEP 177 has a net charge of -0.4750 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: 0.7051879 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 0.7051879 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1991 net assigned charge : 5.470011 assigned positive charge : 327.0330 centred at (gu) : 89.36500 89.51139 90.84877 assigned negative charge : -321.5631 centred at (gu) : 89.22135 89.54054 90.90035 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7065 nv = 96 ne = 84 npr = 42617 no. pairs analyzed = 42617 no. exposed pairs = 2616 no. arc points = 17472 no. surface atoms = 894 nbur = 1233 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4056 m= 7 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8856799E-08 2.2407757E-08 midg,1,midg; midg,igrid,midg 6.4247963E-08 2.7690255E-08 1,midg,midg; igrid,midg,midg -3.0051357E-08 9.9811857E-08 gauss-seidel spectral radius is 0.9895195 estimated iterations to convergence 80 setup time was (sec) 0.4700000 now iterating at: 08:37:36 rms-change max change #iterations 0.2084314 27.86383 at 10iterations 2.5837347E-02 3.888788 at 20iterations 3.6386675E-03 0.4543381 at 30iterations 6.7643286E-04 8.7083817E-02 at 40iterations 1.7870737E-04 2.4505615E-02 at 50iterations finished qdiffx linear iterations at : 08:37:38 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.7870737E-04 2.4505615E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 08:37:39 3.061u 0.141s 0:03.59 89.1% 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 Tue Oct 11 2011 at 08:37:39 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2127 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 !!! WARNING: SEP 177 has a net charge of -0.4750 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: 2.115564 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 2.115564 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1991 net assigned charge : 5.470011 assigned positive charge : 327.0330 centred at (gu) : 88.09482 88.53439 92.54630 assigned negative charge : -321.5631 centred at (gu) : 87.66418 88.62164 92.70113 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 29996 mr = 53360 m= 5763 mr = 22699 m= 545 mr = 3863 m= 14 mr = 283 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 0.5400000 number of dielectric boundary points 31056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15798 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) : 0.7051879 object centre at (A) : -13.30850 30.78400 -1.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0873744E-02 2.5364066E-02 midg,1,midg; midg,igrid,midg 2.7718352E-02 2.9397786E-03 1,midg,midg; igrid,midg,midg 7.1120057E-03 2.7288878E-02 gauss-seidel spectral radius is 0.9988257 estimated iterations to convergence 231 setup time was (sec) 0.8100000 now iterating at: 08:37:40 rms-change max change #iterations 4.717923 189.2394 at 10iterations 2.337314 76.63838 at 20iterations 1.156782 38.27635 at 30iterations 0.5752688 17.75558 at 40iterations 0.2861686 9.145943 at 50iterations 0.1418330 4.436320 at 60iterations 7.0457473E-02 2.149515 at 70iterations 3.5130981E-02 1.046413 at 80iterations 1.7564705E-02 0.5600510 at 90iterations 8.8183740E-03 0.2587433 at 100iterations 4.4727870E-03 0.1422691 at 110iterations 2.3099612E-03 7.6443672E-02 at 120iterations finished qdiffx linear iterations at : 08:37:46 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 2.3099612E-03 7.6443672E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 08:37:47 7.052u 0.188s 0:07.64 94.6% 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 Tue Oct 11 2011 at 08:37:47 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2127 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 !!! WARNING: SEP 177 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.173346 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 3.173346 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1991 net assigned charge : 5.470011 assigned positive charge : 327.0330 centred at (gu) : 87.14240 87.80166 93.81940 assigned negative charge : -321.5631 centred at (gu) : 86.49620 87.93256 94.05155 start vw surface at 0.1300000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 173021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 93467 mr = 128643 m= 38003 mr = 77875 m= 11114 mr = 31208 m= 2203 mr = 8611 m= 268 mr = 1618 m= 11 mr = 155 m= 0 mr = 3 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 69974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15928 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) : 2.115564 object centre at (A) : -13.30850 30.78400 -1.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2660868 0.1594662 midg,1,midg; midg,igrid,midg 0.2356599 -1.0576095E-02 1,midg,midg; igrid,midg,midg 0.2122760 0.2391265 gauss-seidel spectral radius is 0.9992943 estimated iterations to convergence 297 setup time was (sec) 1.960000 now iterating at: 08:37:49 rms-change max change #iterations 10.54574 321.1805 at 10iterations 6.256122 159.7396 at 20iterations 3.695669 80.20332 at 30iterations 2.180354 44.15411 at 40iterations 1.281727 27.14066 at 50iterations 0.7540424 14.21445 at 60iterations 0.4420285 8.675468 at 70iterations 0.2590245 4.782167 at 80iterations 0.1519519 2.752965 at 90iterations 8.9252561E-02 1.771351 at 100iterations 5.2518096E-02 1.111631 at 110iterations 3.0993979E-02 0.5660858 at 120iterations 1.8508401E-02 0.3393841 at 130iterations 1.1229210E-02 0.2075691 at 140iterations 7.0316787E-03 0.1370411 at 150iterations 4.5942152E-03 7.7697754E-02 at 160iterations 3.1728116E-03 5.5408478E-02 at 170iterations 2.3144903E-03 3.7689209E-02 at 180iterations finished qdiffx linear iterations at : 08:37:58 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 2.3144903E-03 3.7689209E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 08:37:59 11.350u 0.184s 0:11.84 97.3% 0+0k 0+0io 0pf+0w