Tue Oct 11 08:36:07 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 08:36:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 0.6501214 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 0.6501214 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 356.0062 centred at (gu) : 90.36868 90.69833 91.95421 assigned negative charge : -354.0067 centred at (gu) : 90.12255 90.54845 91.94144 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 45170 no. pairs analyzed = 45170 no. exposed pairs = 3046 no. arc points = 21303 no. surface atoms = 1017 nbur = 1319 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3753 m= 1 mr = 50 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 0.2800000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2063 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2478976E-09 8.0529903E-09 midg,1,midg; midg,igrid,midg -1.5118186E-08 2.7963081E-08 1,midg,midg; igrid,midg,midg -2.9134743E-08 3.9933429E-08 gauss-seidel spectral radius is 0.9877197 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 08:36:07 rms-change max change #iterations 0.1492533 20.09929 at 10iterations 1.5304713E-02 2.433723 at 20iterations 1.6208618E-03 0.2254179 at 30iterations 1.9521869E-04 2.7484894E-02 at 40iterations 2.8780099E-05 3.7860870E-03 at 50iterations finished qdiffx linear iterations at : 08:36:10 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.8780099E-05 3.7860870E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 08:36:10 3.080u 0.149s 0:03.58 89.9% 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 Tue Oct 11 2011 at 08:36:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 1.950364 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 1.950364 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 356.0062 centred at (gu) : 91.10551 92.09447 95.86217 assigned negative charge : -354.0067 centred at (gu) : 90.36769 91.64527 95.82420 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21303 grid for indexing accessible points = 1.400000 m= 28056 mr = 49855 m= 4907 mr = 20951 m= 318 mr = 3041 m= 3 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17583 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) : 0.6501214 object centre at (A) : 12.19100 -5.540999 18.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7773854E-03 -2.5309562E-03 midg,1,midg; midg,igrid,midg -9.6747559E-03 1.3071912E-02 1,midg,midg; igrid,midg,midg -1.2391542E-02 4.9189910E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.7600000 now iterating at: 08:36:11 rms-change max change #iterations 4.220896 183.7491 at 10iterations 2.005430 73.12712 at 20iterations 0.9536408 29.19421 at 30iterations 0.4519874 14.58325 at 40iterations 0.2148197 7.082213 at 50iterations 0.1014308 3.466728 at 60iterations 4.8039980E-02 1.481203 at 70iterations 2.2883523E-02 0.7471661 at 80iterations 1.0873401E-02 0.3530273 at 90iterations 5.1555661E-03 0.1626263 at 100iterations 2.4562068E-03 7.9086781E-02 at 110iterations 1.1802934E-03 3.6008835E-02 at 120iterations finished qdiffx linear iterations at : 08:36:17 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 1.1802934E-03 3.6008835E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 08:36:18 6.860u 0.156s 0:07.33 95.6% 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 08:36:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 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: 2.925546 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): -12.55300 36.93500 ymin,ymax (A): -27.32800 16.24600 zmin,zma (A): -9.229000 45.53000 x,y,z range (A): 49.48800 43.57400 54.75900 scale (grids/A): 2.925546 object centre (A): 12.19100 -5.540999 18.15050 number of atom coordinates read : 2336 total number of charged atoms : 2230 net assigned charge : 2.000011 assigned positive charge : 356.0062 centred at (gu) : 91.65816 93.14153 98.79309 assigned negative charge : -354.0067 centred at (gu) : 90.55150 92.46786 98.73626 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21303 grid for indexing accessible points = 1.400000 m= 88359 mr = 120484 m= 34437 mr = 72470 m= 8879 mr = 27862 m= 1402 mr = 6623 m= 84 mr = 927 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 71464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 17840 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) : 1.950364 object centre at (A) : 12.19100 -5.540999 18.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4118120E-02 9.1217011E-02 midg,1,midg; midg,igrid,midg -0.1018467 8.0633625E-02 1,midg,midg; igrid,midg,midg -0.1077590 0.4415326 gauss-seidel spectral radius is 0.9992637 estimated iterations to convergence 291 setup time was (sec) 1.590000 now iterating at: 08:36:20 rms-change max change #iterations 9.827118 347.6265 at 10iterations 5.728721 136.8753 at 20iterations 3.331989 82.20887 at 30iterations 1.932613 39.59045 at 40iterations 1.119308 22.92212 at 50iterations 0.6481720 13.17023 at 60iterations 0.3742879 7.039885 at 70iterations 0.2160081 4.055243 at 80iterations 0.1243063 2.255316 at 90iterations 7.1858965E-02 1.327812 at 100iterations 4.1414507E-02 0.7819252 at 110iterations 2.3927618E-02 0.5135536 at 120iterations 1.3808649E-02 0.2629528 at 130iterations 7.9554087E-03 0.1375523 at 140iterations 4.6211197E-03 8.0992699E-02 at 150iterations 2.6894584E-03 4.6875000E-02 at 160iterations 1.5797914E-03 2.9823303E-02 at 170iterations 9.4290945E-04 1.7619133E-02 at 180iterations finished qdiffx linear iterations at : 08:36:29 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 9.4290945E-04 1.7619133E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 08:36:29 11.189u 0.170s 0:11.67 97.2% 0+0k 0+0io 0pf+0w