Tue Oct 11 08:23:04 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 08:23:04 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: THR 174 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 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: 0.6065665 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 0.6065665 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2661 net assigned charge : 3.767012 assigned positive charge : 430.7969 centred at (gu) : 90.39910 90.33739 92.30154 assigned negative charge : -427.0302 centred at (gu) : 90.15611 90.16199 92.31487 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6849 nv = 96 ne = 84 npr = 57031 no. pairs analyzed = 57031 no. exposed pairs = 3339 no. arc points = 23600 no. surface atoms = 1122 nbur = 1695 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3845 m= 0 mr = 33 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3300000 number of dielectric boundary points 3274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8443 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5701819E-09 2.1023641E-09 midg,1,midg; midg,igrid,midg -6.2842798E-09 1.1149699E-08 1,midg,midg; igrid,midg,midg -9.3536823E-09 1.4753275E-08 gauss-seidel spectral radius is 0.9859441 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 08:23:05 rms-change max change #iterations 0.1251931 17.22315 at 10iterations 1.0951684E-02 1.656822 at 20iterations 1.0269260E-03 0.1486893 at 30iterations 1.2866905E-04 1.9906044E-02 at 40iterations 3.2458956E-05 5.8298111E-03 at 50iterations finished qdiffx linear iterations at : 08:23:08 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.2458956E-05 5.8298111E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:23:09 3.419u 0.170s 0:04.42 80.9% 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 08:23:09 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: THR 174 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 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: 1.819700 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 1.819700 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2661 net assigned charge : 3.767012 assigned positive charge : 430.7969 centred at (gu) : 91.19711 91.01158 96.90401 assigned negative charge : -427.0302 centred at (gu) : 90.46792 90.48566 96.94452 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 26309 mr = 52813 m= 3544 mr = 19603 m= 172 mr = 2102 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 0.5500000 number of dielectric boundary points 30097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20786 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) : 0.6065665 object centre at (A) : 12.26450 27.65350 16.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1854397E-03 6.5628090E-03 midg,1,midg; midg,igrid,midg -1.3793204E-02 1.5096433E-02 1,midg,midg; igrid,midg,midg -9.4964672E-03 3.6450103E-02 gauss-seidel spectral radius is 0.9985271 estimated iterations to convergence 207 setup time was (sec) 0.8500000 now iterating at: 08:23:10 rms-change max change #iterations 4.143474 169.4109 at 10iterations 1.883426 69.23532 at 20iterations 0.8601116 32.29180 at 30iterations 0.3921291 13.36119 at 40iterations 0.1785623 6.771969 at 50iterations 8.1456460E-02 2.574440 at 60iterations 3.7203483E-02 1.144737 at 70iterations 1.6950097E-02 0.5844536 at 80iterations 7.7486136E-03 0.2467237 at 90iterations 3.5516182E-03 0.1169928 at 100iterations 1.6395209E-03 5.2619934E-02 at 110iterations 7.6504273E-04 2.5985718E-02 at 120iterations finished qdiffx linear iterations at : 08:23:17 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 7.6504273E-04 2.5985718E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 08:23:18 8.072u 0.186s 0:08.67 95.1% 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 08:23:18 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: THR 174 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 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: 2.729550 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 2.729550 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2661 net assigned charge : 3.767012 assigned positive charge : 430.7969 centred at (gu) : 91.79545 91.51725 100.3557 assigned negative charge : -427.0302 centred at (gu) : 90.70184 90.72854 100.4167 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 173108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 87399 mr = 127983 m= 29571 mr = 72242 m= 6224 mr = 23889 m= 719 mr = 4563 m= 40 mr = 449 m= 0 mr = 16 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 3906 time to turn everything in is 1.450000 number of dielectric boundary points 67919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 21287 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) : 1.819700 object centre at (A) : 12.26450 27.65350 16.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1629085 0.2381405 midg,1,midg; midg,igrid,midg -0.1716806 0.1846588 1,midg,midg; igrid,midg,midg -9.2488095E-02 0.3241827 gauss-seidel spectral radius is 0.9992248 estimated iterations to convergence 284 setup time was (sec) 1.790000 now iterating at: 08:23:20 rms-change max change #iterations 9.846926 331.8016 at 10iterations 5.687712 158.2581 at 20iterations 3.271403 69.51540 at 30iterations 1.878605 52.28797 at 40iterations 1.075721 23.49104 at 50iterations 0.6139720 11.68876 at 60iterations 0.3495952 7.679614 at 70iterations 0.1993077 3.615747 at 80iterations 0.1135142 2.075655 at 90iterations 6.4570233E-02 1.221924 at 100iterations 3.6693141E-02 0.7201242 at 110iterations 2.0855015E-02 0.3742218 at 120iterations 1.1854472E-02 0.2353344 at 130iterations 6.7300433E-03 0.1448669 at 140iterations 3.8334311E-03 7.3999405E-02 at 150iterations 2.1785430E-03 4.2865753E-02 at 160iterations 1.2383462E-03 2.4532318E-02 at 170iterations 7.0700515E-04 1.4849663E-02 at 180iterations finished qdiffx linear iterations at : 08:23:31 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 7.0700515E-04 1.4849663E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 08:23:32 13.479u 0.200s 0:14.16 96.5% 0+0k 0+0io 0pf+0w