Mon Oct 10 17:15:11 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 17:15:11 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: ASN 315 has a net charge of -0.0550 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6066803 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 0.6066803 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2724 net assigned charge : -0.6489890 assigned positive charge : 430.3283 centred at (gu) : 91.59209 89.34754 88.95387 assigned negative charge : -430.9779 centred at (gu) : 91.54447 89.40699 88.91267 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7135 nv = 96 ne = 84 npr = 56899 no. pairs analyzed = 56899 no. exposed pairs = 3943 no. arc points = 26779 no. surface atoms = 1308 nbur = 1564 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3743 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0893288E-09 1.2968966E-09 midg,1,midg; midg,igrid,midg 2.9569915E-09 -2.8850242E-09 1,midg,midg; igrid,midg,midg -1.9226096E-09 2.8475147E-09 gauss-seidel spectral radius is 0.9859653 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 17:15:12 rms-change max change #iterations 0.1187814 18.37586 at 10iterations 1.0392063E-02 1.719991 at 20iterations 9.6785981E-04 0.1436787 at 30iterations 1.0273665E-04 1.5892029E-02 at 40iterations 1.7570283E-05 2.5873184E-03 at 50iterations finished qdiffx linear iterations at : 17:15:14 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.7570283E-05 2.5873184E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:15:15 3.171u 0.127s 0:03.78 87.0% 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 17:15:15 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 1.820041 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 1.820041 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2724 net assigned charge : -0.6489890 assigned positive charge : 430.3283 centred at (gu) : 94.77588 88.04197 86.86063 assigned negative charge : -430.9779 centred at (gu) : 94.63294 88.22044 86.73749 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26779 grid for indexing accessible points = 1.400000 m= 26111 mr = 52104 m= 3691 mr = 18437 m= 168 mr = 2094 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.5300000 number of dielectric boundary points 34505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21301 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) : 0.6066803 object centre at (A) : -5.344501 65.17750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2969571E-02 -4.6259474E-02 midg,1,midg; midg,igrid,midg 6.8636327E-03 -1.0215777E-03 1,midg,midg; igrid,midg,midg -1.4935943E-02 1.0916767E-02 gauss-seidel spectral radius is 0.9985443 estimated iterations to convergence 208 setup time was (sec) 0.8000000 now iterating at: 17:15:16 rms-change max change #iterations 4.110909 169.2059 at 10iterations 1.867356 70.32996 at 20iterations 0.8535535 27.45915 at 30iterations 0.3904219 12.81985 at 40iterations 0.1775005 5.565057 at 50iterations 8.1140988E-02 2.624039 at 60iterations 3.6974404E-02 1.141075 at 70iterations 1.6905850E-02 0.4894364 at 80iterations 7.7333744E-03 0.2948284 at 90iterations 3.5379087E-03 0.1207714 at 100iterations 1.6176488E-03 5.0163269E-02 at 110iterations 7.3872978E-04 2.3423672E-02 at 120iterations finished qdiffx linear iterations at : 17:15:22 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 7.3872978E-04 2.3423672E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:15:22 7.058u 0.188s 0:07.52 96.1% 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 Mon Oct 10 2011 at 17:15:22 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 2.730062 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): -33.10800 22.41900 ymin,ymax (A): 40.26600 90.08900 zmin,zma (A): 0.3040000 58.98400 x,y,z range (A): 55.52700 49.82299 58.68000 scale (grids/A): 2.730062 object centre (A): -5.344501 65.17750 29.64400 number of atom coordinates read : 2872 total number of charged atoms : 2724 net assigned charge : -0.6489890 assigned positive charge : 430.3283 centred at (gu) : 97.16357 87.06273 85.29091 assigned negative charge : -430.9779 centred at (gu) : 96.94907 87.33055 85.10597 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 178739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26779 grid for indexing accessible points = 1.400000 m= 86199 mr = 127294 m= 28898 mr = 68417 m= 6283 mr = 22434 m= 709 mr = 4423 m= 27 mr = 417 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 613 time to turn everything in is 1.310000 number of dielectric boundary points 77870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 21791 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) : 1.820041 object centre at (A) : -5.344501 65.17750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3768224 -0.8841943 midg,1,midg; midg,igrid,midg 6.6174358E-02 -1.7880300E-02 1,midg,midg; igrid,midg,midg -9.7487845E-02 0.2246595 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.590000 now iterating at: 17:15:24 rms-change max change #iterations 10.07195 300.9009 at 10iterations 5.953065 148.8307 at 20iterations 3.483670 87.22443 at 30iterations 2.027677 54.03022 at 40iterations 1.175743 24.12204 at 50iterations 0.6798663 14.23609 at 60iterations 0.3929440 7.997531 at 70iterations 0.2259592 4.382849 at 80iterations 0.1304152 2.674588 at 90iterations 7.4664697E-02 1.447163 at 100iterations 4.2910367E-02 0.8394165 at 110iterations 2.4655102E-02 0.4644270 at 120iterations 1.4127303E-02 0.2846394 at 130iterations 8.1002805E-03 0.1505337 at 140iterations 4.6368050E-03 8.3559036E-02 at 150iterations 2.6564884E-03 4.8183441E-02 at 160iterations 1.5199038E-03 2.6161194E-02 at 170iterations 8.7248941E-04 1.5867233E-02 at 180iterations finished qdiffx linear iterations at : 17:15:34 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 8.7248941E-04 1.5867233E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 17:15:34 11.517u 0.185s 0:12.12 96.4% 0+0k 0+0io 0pf+0w