Tue Oct 11 03:19:29 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+sph.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 = amb.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 03:19:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 0.6089843 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 0.6089843 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.999989 assigned positive charge : 398.0887 centred at (gu) : 88.99676 87.58616 92.19622 assigned negative charge : -401.0896 centred at (gu) : 88.98709 87.53923 92.11150 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 52459 no. pairs analyzed = 52459 no. exposed pairs = 3828 no. arc points = 27498 no. surface atoms = 1262 nbur = 1443 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3344 m= 0 mr = 23 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2710 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6308818E-09 4.0290642E-09 midg,1,midg; midg,igrid,midg -6.9682251E-09 2.9772204E-10 1,midg,midg; igrid,midg,midg -2.7415061E-09 -1.0131219E-09 gauss-seidel spectral radius is 0.9860640 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 03:19:30 rms-change max change #iterations 0.1159385 17.00318 at 10iterations 9.9957986E-03 1.715546 at 20iterations 8.9534384E-04 0.1293144 at 30iterations 7.8492252E-05 1.1675835E-02 at 40iterations 8.7935541E-06 1.3557673E-03 at 50iterations finished qdiffx linear iterations at : 03:19:33 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 8.7935541E-06 1.3557673E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:19:33 3.583u 0.190s 0:04.35 86.6% 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 03:19:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 1.826953 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 1.826953 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.999989 assigned positive charge : 398.0887 centred at (gu) : 86.98955 82.75780 96.58833 assigned negative charge : -401.0896 centred at (gu) : 86.96130 82.61750 96.33445 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27498 grid for indexing accessible points = 1.400000 m= 24585 mr = 48255 m= 3035 mr = 16713 m= 135 mr = 1564 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 295 time to turn everything in is 0.5700000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20040 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) : 0.6089843 object centre at (A) : -1.846499 37.33200 -3.400000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0180989E-02 3.6677420E-02 midg,1,midg; midg,igrid,midg -3.7706383E-02 -2.7664352E-02 1,midg,midg; igrid,midg,midg 1.2154281E-03 3.9680684E-03 gauss-seidel spectral radius is 0.9985462 estimated iterations to convergence 208 setup time was (sec) 0.8900000 now iterating at: 03:19:35 rms-change max change #iterations 3.979903 188.8189 at 10iterations 1.814219 65.71548 at 20iterations 0.8240505 28.38194 at 30iterations 0.3754195 11.49095 at 40iterations 0.1715650 6.243267 at 50iterations 7.8034341E-02 2.394509 at 60iterations 3.5652399E-02 1.320105 at 70iterations 1.6290164E-02 0.5832939 at 80iterations 7.4439500E-03 0.2588041 at 90iterations 3.4112164E-03 0.1110840 at 100iterations 1.5549185E-03 5.4199219E-02 at 110iterations 7.0967252E-04 2.2703648E-02 at 120iterations finished qdiffx linear iterations at : 03:19:41 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 7.0967252E-04 2.2703648E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 03:19:42 8.009u 0.239s 0:08.64 95.2% 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 03:19:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 2.740429 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 2.740429 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.999989 assigned positive charge : 398.0887 centred at (gu) : 85.48400 79.13655 99.88231 assigned negative charge : -401.0896 centred at (gu) : 85.44187 78.92616 99.50153 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 171685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27498 grid for indexing accessible points = 1.400000 m= 81404 mr = 118060 m= 26198 mr = 63358 m= 5042 mr = 19623 m= 534 mr = 3332 m= 18 mr = 276 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 1.400000 number of dielectric boundary points 80230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 20436 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) : 1.826953 object centre at (A) : -1.846499 37.33200 -3.400000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7406498 0.4194632 midg,1,midg; midg,igrid,midg -0.2288590 -0.5326642 1,midg,midg; igrid,midg,midg -2.0644525E-02 2.9223764E-02 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.740000 now iterating at: 03:19:44 rms-change max change #iterations 9.761346 289.5950 at 10iterations 5.790819 130.8173 at 20iterations 3.408358 82.66217 at 30iterations 1.997384 49.00283 at 40iterations 1.167038 26.41397 at 50iterations 0.6782291 13.19720 at 60iterations 0.3932520 8.718750 at 70iterations 0.2273604 4.877276 at 80iterations 0.1313730 2.527710 at 90iterations 7.5972669E-02 1.376791 at 100iterations 4.3768451E-02 0.8539963 at 110iterations 2.5265904E-02 0.5784302 at 120iterations 1.4537455E-02 0.2916265 at 130iterations 8.3545661E-03 0.1999359 at 140iterations 4.8208772E-03 9.3252182E-02 at 150iterations 2.7709110E-03 4.9823761E-02 at 160iterations 1.5986243E-03 2.9281616E-02 at 170iterations 9.2143117E-04 1.8862247E-02 at 180iterations finished qdiffx linear iterations at : 03:19:57 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 9.2143117E-04 1.8862247E-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) 14.56000 DelPhi exited at 03:19:57 14.565u 0.298s 0:15.27 97.2% 0+0k 0+0io 0pf+0w