Mon Oct 10 14:17:00 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 14:17:00 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: GLM 268 has a net charge of -0.0940 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: 0.6407141 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 0.6407141 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2457 net assigned charge : 5.406009 assigned positive charge : 401.0896 centred at (gu) : 90.44434 90.20240 91.05099 assigned negative charge : -395.6843 centred at (gu) : 90.39813 90.04300 91.16088 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7174 nv = 96 ne = 84 npr = 50862 no. pairs analyzed = 50862 no. exposed pairs = 3389 no. arc points = 23750 no. surface atoms = 1145 nbur = 1460 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3765 m= 5 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2468 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7033008E-08 -6.8489379E-09 midg,1,midg; midg,igrid,midg -1.0996116E-08 2.8317091E-08 1,midg,midg; igrid,midg,midg 2.3173181E-09 1.5057557E-08 gauss-seidel spectral radius is 0.9873824 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 14:17:01 rms-change max change #iterations 0.1504851 21.26582 at 10iterations 1.5742242E-02 2.529942 at 20iterations 2.1670556E-03 0.3936462 at 30iterations 5.1839859E-04 8.6967468E-02 at 40iterations 1.5767482E-04 2.5634766E-02 at 50iterations finished qdiffx linear iterations at : 14:17:04 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.5767482E-04 2.5634766E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:17:05 3.587u 0.244s 0:04.19 91.1% 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 14:17:05 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: GLM 268 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.922142 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 1.922142 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2457 net assigned charge : 5.406009 assigned positive charge : 401.0896 centred at (gu) : 91.33260 90.60667 93.15228 assigned negative charge : -395.6843 centred at (gu) : 91.19382 90.12850 93.48251 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 77484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23750 grid for indexing accessible points = 1.400000 m= 26975 mr = 52613 m= 3968 mr = 19086 m= 256 mr = 2224 m= 7 mr = 105 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 0.5300000 number of dielectric boundary points 34662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19311 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) : 0.6407141 object centre at (A) : 13.52100 0.1914988 27.33850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7563415E-02 8.3849235E-03 midg,1,midg; midg,igrid,midg -2.8134601E-02 1.8238576E-02 1,midg,midg; igrid,midg,midg 1.1120125E-02 1.9047443E-03 gauss-seidel spectral radius is 0.9986686 estimated iterations to convergence 217 setup time was (sec) 0.8600000 now iterating at: 14:17:06 rms-change max change #iterations 4.396856 183.5597 at 10iterations 2.082455 73.66746 at 20iterations 0.9825764 30.32117 at 30iterations 0.4657078 14.83382 at 40iterations 0.2198849 6.962592 at 50iterations 0.1039656 3.720384 at 60iterations 4.9288455E-02 1.570743 at 70iterations 2.3459300E-02 0.7176267 at 80iterations 1.1309523E-02 0.3661447 at 90iterations 5.5273492E-03 0.1779442 at 100iterations 2.7771946E-03 9.5321655E-02 at 110iterations 1.4578967E-03 5.6121826E-02 at 120iterations finished qdiffx linear iterations at : 14:17:14 total time elapsed so far: 8.750000 # loops : 120 mean,max change (kT/e) : 1.4578967E-03 5.6121826E-02 energy calculations done at 8.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 14:17:14 8.936u 0.326s 0:09.60 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 14:17:14 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: GLM 268 has a net charge of -0.0940 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: 2.883214 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 2.883214 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2457 net assigned charge : 5.406009 assigned positive charge : 401.0896 centred at (gu) : 91.99866 90.90981 94.72833 assigned negative charge : -395.6843 centred at (gu) : 91.79066 90.19279 95.22346 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 179361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23750 grid for indexing accessible points = 1.400000 m= 88619 mr = 128184 m= 30035 mr = 71059 m= 6735 mr = 23134 m= 1128 mr = 4669 m= 74 mr = 772 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 78118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19656 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) : 1.922142 object centre at (A) : 13.52100 0.1914988 27.33850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5389230 -0.1081927 midg,1,midg; midg,igrid,midg -0.3756828 0.1934993 1,midg,midg; igrid,midg,midg 0.2080633 -2.2353374E-03 gauss-seidel spectral radius is 0.9992721 estimated iterations to convergence 292 setup time was (sec) 1.740000 now iterating at: 14:17:16 rms-change max change #iterations 10.43771 422.8820 at 10iterations 6.210138 156.2474 at 20iterations 3.662829 71.12901 at 30iterations 2.146908 43.33080 at 40iterations 1.254505 24.87292 at 50iterations 0.7339496 14.14390 at 60iterations 0.4276939 7.452800 at 70iterations 0.2487067 4.648993 at 80iterations 0.1445995 2.846701 at 90iterations 8.3901629E-02 1.698757 at 100iterations 4.8778821E-02 0.8703766 at 110iterations 2.8449863E-02 0.4901800 at 120iterations 1.6648056E-02 0.3134215 at 130iterations 9.8490724E-03 0.1823578 at 140iterations 5.9064357E-03 0.1111259 at 150iterations 3.6425598E-03 7.4020386E-02 at 160iterations 2.3482519E-03 4.7714233E-02 at 170iterations 1.5969145E-03 3.5440445E-02 at 180iterations finished qdiffx linear iterations at : 14:17:29 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 1.5969145E-03 3.5440445E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 14:17:29 14.544u 0.302s 0:15.20 97.6% 0+0k 0+0io 0pf+0w