Tue Nov 22 14:11:50 PST 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 Nov 22 2011 at 14:11:55 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5763035 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 0.5763035 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 90.37099 89.56972 89.92985 assigned negative charge : -289.2262 centred at (gu) : 90.28390 89.68616 89.91470 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4246 nv = 96 ne = 84 npr = 40694 no. pairs analyzed = 40694 no. exposed pairs = 2472 no. arc points = 17347 no. surface atoms = 844 nbur = 1120 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 194 mr = 2258 m= 0 mr = 15 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1500000 number of dielectric boundary points 2167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1771 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7968564E-10 7.4541212E-10 midg,1,midg; midg,igrid,midg 2.2382427E-09 -8.3662738E-10 1,midg,midg; igrid,midg,midg -5.0023868E-10 1.8101577E-09 gauss-seidel spectral radius is 0.9843758 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 14:11:58 rms-change max change #iterations 7.3962554E-02 14.50774 at 10iterations 5.7233754E-03 1.046691 at 20iterations 4.3945352E-04 7.6714516E-02 at 30iterations 3.2942880E-05 5.5122375E-03 at 40iterations 2.5559423E-06 4.8065186E-04 at 50iterations finished qdiffx linear iterations at : 14:12:08 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 2.5559423E-06 4.8065186E-04 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 14:12:10 3.854u 0.247s 0:15.88 25.7% 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 Nov 22 2011 at 14:12:11 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.728911 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 1.728911 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 91.11266 88.70914 89.78955 assigned negative charge : -289.2262 centred at (gu) : 90.85172 89.05880 89.74419 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 46349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 15297 mr = 31205 m= 1826 mr = 11115 m= 59 mr = 1065 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 1394 time to turn everything in is 0.2500000 number of dielectric boundary points 20132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14210 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) : 0.5763035 object centre at (A) : -12.37900 21.09250 27.84450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1273592E-02 2.2913318E-02 midg,1,midg; midg,igrid,midg 1.9856023E-03 -5.7075950E-03 1,midg,midg; igrid,midg,midg -1.4606330E-03 -8.3969778E-04 gauss-seidel spectral radius is 0.9982638 estimated iterations to convergence 191 setup time was (sec) 0.4900000 now iterating at: 14:12:16 rms-change max change #iterations 3.016955 164.5047 at 10iterations 1.267658 68.38943 at 20iterations 0.5402708 24.04619 at 30iterations 0.2301408 9.629963 at 40iterations 9.7607508E-02 4.550403 at 50iterations 4.1381549E-02 1.684135 at 60iterations 1.7586680E-02 0.6820302 at 70iterations 7.4810390E-03 0.3014030 at 80iterations 3.1871570E-03 0.1222134 at 90iterations 1.3507408E-03 6.4069271E-02 at 100iterations 5.7326443E-04 2.5641441E-02 at 110iterations 2.4407277E-04 1.0723114E-02 at 120iterations finished qdiffx linear iterations at : 14:12:38 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 2.4407277E-04 1.0723114E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 14:12:38 8.150u 0.222s 0:27.31 30.6% 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 Nov 22 2011 at 14:12:41 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.593366 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 2.593366 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 91.66911 88.06364 89.68427 assigned negative charge : -289.2262 centred at (gu) : 91.27754 88.58827 89.61638 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 107475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 50810 mr = 75895 m= 16497 mr = 41142 m= 3124 mr = 13293 m= 308 mr = 2270 m= 6 mr = 198 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4537 time to turn everything in is 0.6400000 number of dielectric boundary points 45420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14652 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) : 1.728911 object centre at (A) : -12.37900 21.09250 27.84450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2327258 0.2428584 midg,1,midg; midg,igrid,midg -2.8457439E-03 -8.7227911E-02 1,midg,midg; igrid,midg,midg -3.7973687E-02 -4.2454861E-02 gauss-seidel spectral radius is 0.9991280 estimated iterations to convergence 268 setup time was (sec) 0.9200000 now iterating at: 14:12:44 rms-change max change #iterations 7.365479 284.5526 at 10iterations 4.069377 127.0006 at 20iterations 2.231214 60.34726 at 30iterations 1.223862 28.75232 at 40iterations 0.6706038 15.11863 at 50iterations 0.3654833 8.881264 at 60iterations 0.1994698 4.684395 at 70iterations 0.1093039 2.729675 at 80iterations 5.9491556E-02 1.363607 at 90iterations 3.2570891E-02 0.7959843 at 100iterations 1.7741973E-02 0.4185219 at 110iterations 9.7207781E-03 0.2251205 at 120iterations 5.3038551E-03 0.1199088 at 130iterations 2.8961981E-03 6.7489624E-02 at 140iterations 1.5790414E-03 3.7860394E-02 at 150iterations 8.6378970E-04 1.9706726E-02 at 160iterations 4.7165563E-04 1.0515213E-02 at 170iterations 2.5745441E-04 6.1631203E-03 at 180iterations finished qdiffx linear iterations at : 14:13:23 total time elapsed so far: 13.83000 # loops : 180 mean,max change (kT/e) : 2.5745441E-04 6.1631203E-03 energy calculations done at 13.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 14:13:25 13.971u 0.285s 0:44.94 31.7% 0+0k 0+0io 0pf+0w