Tue Oct 11 00:32:56 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 00:32:56 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: GLM 266 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6272575 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 0.6272575 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2475 net assigned charge : 7.906016 assigned positive charge : 396.2408 centred at (gu) : 89.86286 90.97163 89.95459 assigned negative charge : -388.3354 centred at (gu) : 89.87979 90.76443 90.08208 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6768 nv = 96 ne = 84 npr = 53311 no. pairs analyzed = 53311 no. exposed pairs = 3082 no. arc points = 21429 no. surface atoms = 1037 nbur = 1583 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 3857 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3400000 number of dielectric boundary points 3229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8229919E-08 -2.8057081E-09 midg,1,midg; midg,igrid,midg -7.6802529E-09 3.0130771E-08 1,midg,midg; igrid,midg,midg 9.4081463E-09 6.1864891E-09 gauss-seidel spectral radius is 0.9868326 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 00:32:57 rms-change max change #iterations 0.1357096 21.10046 at 10iterations 1.3484382E-02 2.835625 at 20iterations 1.7049065E-03 0.3148651 at 30iterations 3.5311916E-04 7.8319550E-02 at 40iterations 8.8458626E-05 2.0816803E-02 at 50iterations finished qdiffx linear iterations at : 00:33:01 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 8.8458626E-05 2.0816803E-02 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 00:33:01 4.198u 0.243s 0:04.78 92.6% 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 00:33:01 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: GLM 266 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.881773 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 1.881773 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2475 net assigned charge : 7.906016 assigned positive charge : 396.2408 centred at (gu) : 89.58807 92.91447 89.86301 assigned negative charge : -388.3354 centred at (gu) : 89.63906 92.29296 90.24612 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21429 grid for indexing accessible points = 1.400000 m= 26860 mr = 52028 m= 4188 mr = 20332 m= 200 mr = 2744 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2059 time to turn everything in is 0.5400000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19400 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) : 0.6272575 object centre at (A) : 34.73450 28.14350 31.04200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0927490E-02 5.6278543E-03 midg,1,midg; midg,igrid,midg -3.5688248E-02 3.0940140E-02 1,midg,midg; igrid,midg,midg 3.8732814E-03 9.8605435E-03 gauss-seidel spectral radius is 0.9985988 estimated iterations to convergence 212 setup time was (sec) 0.8600000 now iterating at: 00:33:02 rms-change max change #iterations 4.186355 183.6379 at 10iterations 1.925811 68.58480 at 20iterations 0.8946623 29.87456 at 30iterations 0.4154924 13.31744 at 40iterations 0.1928858 6.167667 at 50iterations 8.9774743E-02 3.196591 at 60iterations 4.1682489E-02 1.278228 at 70iterations 1.9475460E-02 0.6029663 at 80iterations 9.2022717E-03 0.2932358 at 90iterations 4.4141035E-03 0.1501694 at 100iterations 2.1754827E-03 8.3953857E-02 at 110iterations 1.1247958E-03 4.6306610E-02 at 120iterations finished qdiffx linear iterations at : 00:33:11 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.1247958E-03 4.6306610E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 00:33:11 9.427u 0.245s 0:09.94 97.1% 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 00:33:11 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: GLM 266 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.822659 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 2.822659 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2475 net assigned charge : 7.906016 assigned positive charge : 396.2408 centred at (gu) : 89.38198 94.37158 89.79428 assigned negative charge : -388.3354 centred at (gu) : 89.45845 93.43935 90.36909 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21429 grid for indexing accessible points = 1.400000 m= 86544 mr = 125465 m= 31815 mr = 71842 m= 7583 mr = 26235 m= 942 mr = 5937 m= 32 mr = 581 m= 0 mr = 11 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7228 time to turn everything in is 1.400000 number of dielectric boundary points 66979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 19799 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) : 1.881773 object centre at (A) : 34.73450 28.14350 31.04200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3105374 7.0522845E-02 midg,1,midg; midg,igrid,midg -0.7416008 0.1156562 1,midg,midg; igrid,midg,midg -8.5696587E-03 -1.9543211E-03 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.740000 now iterating at: 00:33:13 rms-change max change #iterations 9.785969 327.8345 at 10iterations 5.648947 129.6161 at 20iterations 3.230779 65.15389 at 30iterations 1.853994 35.99267 at 40iterations 1.062492 24.59229 at 50iterations 0.6052585 12.13018 at 60iterations 0.3468207 6.734249 at 70iterations 0.1981316 3.698700 at 80iterations 0.1133056 2.203642 at 90iterations 6.4824991E-02 1.264166 at 100iterations 3.7109733E-02 0.7363739 at 110iterations 2.1297045E-02 0.4442997 at 120iterations 1.2280671E-02 0.2489204 at 130iterations 7.1473485E-03 0.1434441 at 140iterations 4.2253993E-03 9.2765808E-02 at 150iterations 2.5695062E-03 6.6715240E-02 at 160iterations 1.6320215E-03 4.0679932E-02 at 170iterations 1.0961881E-03 2.7103424E-02 at 180iterations finished qdiffx linear iterations at : 00:33:26 total time elapsed so far: 14.88000 # loops : 180 mean,max change (kT/e) : 1.0961881E-03 2.7103424E-02 energy calculations done at 14.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 00:33:27 15.057u 0.250s 0:15.57 98.2% 0+0k 0+0io 0pf+0w