Mon Oct 10 20:16:08 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 Mon Oct 10 2011 at 20:16:08 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 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: 0.5964249 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 0.5964249 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000027 assigned positive charge : 415.5935 centred at (gu) : 90.09390 89.12939 90.47948 assigned negative charge : -414.5946 centred at (gu) : 90.13811 89.15914 90.53860 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6563 nv = 96 ne = 84 npr = 55270 no. pairs analyzed = 55270 no. exposed pairs = 3897 no. arc points = 27701 no. surface atoms = 1289 nbur = 1488 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3183 m= 0 mr = 17 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2788 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1770061E-09 -1.8932746E-09 midg,1,midg; midg,igrid,midg 1.7326974E-09 -5.3326638E-10 1,midg,midg; igrid,midg,midg 1.8761026E-09 -1.1906524E-09 gauss-seidel spectral radius is 0.9854773 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 20:16:09 rms-change max change #iterations 0.1070696 19.27014 at 10iterations 9.1581112E-03 1.360660 at 20iterations 8.9907378E-04 0.1505384 at 30iterations 1.3533322E-04 2.3014069E-02 at 40iterations 2.9490429E-05 4.8542023E-03 at 50iterations finished qdiffx linear iterations at : 20:16:12 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.9490429E-05 4.8542023E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 20:16:12 3.363u 0.128s 0:04.15 83.8% 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 Mon Oct 10 2011 at 20:16:13 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 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: 1.789275 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 1.789275 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000027 assigned positive charge : 415.5935 centred at (gu) : 90.28111 87.38786 91.43794 assigned negative charge : -414.5946 centred at (gu) : 90.41404 87.47708 91.61574 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 23898 mr = 44828 m= 3452 mr = 16394 m= 117 mr = 1873 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.5800000 number of dielectric boundary points 34277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20581 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) : 0.5964249 object centre at (A) : 15.07800 59.81750 15.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3694364E-04 -3.1172842E-02 midg,1,midg; midg,igrid,midg 1.4592161E-02 -8.3728209E-03 1,midg,midg; igrid,midg,midg 1.4586468E-02 -1.9618394E-03 gauss-seidel spectral radius is 0.9984943 estimated iterations to convergence 204 setup time was (sec) 0.8900000 now iterating at: 20:16:14 rms-change max change #iterations 3.919234 198.2469 at 10iterations 1.752231 64.78401 at 20iterations 0.7852209 27.90961 at 30iterations 0.3543366 12.53713 at 40iterations 0.1592042 5.243221 at 50iterations 7.1580879E-02 2.308428 at 60iterations 3.2280039E-02 1.171387 at 70iterations 1.4563201E-02 0.4755859 at 80iterations 6.6149598E-03 0.2606010 at 90iterations 2.9947185E-03 0.1002302 at 100iterations 1.3692050E-03 4.4841766E-02 at 110iterations 6.3679856E-04 2.1909714E-02 at 120iterations finished qdiffx linear iterations at : 20:16:21 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 6.3679856E-04 2.1909714E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 20:16:21 7.966u 0.222s 0:08.62 94.8% 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 Mon Oct 10 2011 at 20:16:21 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.683912 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 2.683912 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000027 assigned positive charge : 415.5935 centred at (gu) : 90.42154 86.08175 92.15659 assigned negative charge : -414.5946 centred at (gu) : 90.62109 86.21561 92.42356 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 161874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 76780 mr = 110326 m= 27174 mr = 59492 m= 5823 mr = 20790 m= 488 mr = 3995 m= 10 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 475 time to turn everything in is 1.350000 number of dielectric boundary points 77333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 21106 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) : 1.789275 object centre at (A) : 15.07800 59.81750 15.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4153149E-02 -0.4681512 midg,1,midg; midg,igrid,midg 0.3231773 -3.4142930E-02 1,midg,midg; igrid,midg,midg 0.1511224 -5.7176121E-02 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.690000 now iterating at: 20:16:23 rms-change max change #iterations 9.641351 403.3166 at 10iterations 5.636711 140.3118 at 20iterations 3.256970 76.94557 at 30iterations 1.877699 39.03613 at 40iterations 1.081676 22.35481 at 50iterations 0.6180989 13.50521 at 60iterations 0.3539104 6.950397 at 70iterations 0.2028363 3.750652 at 80iterations 0.1155679 2.581970 at 90iterations 6.6050678E-02 1.300817 at 100iterations 3.7675325E-02 0.7421751 at 110iterations 2.1488125E-02 0.4348450 at 120iterations 1.2282969E-02 0.2323227 at 130iterations 7.0094238E-03 0.1307526 at 140iterations 4.0163128E-03 7.7013016E-02 at 150iterations 2.3129529E-03 5.3211212E-02 at 160iterations 1.3475259E-03 2.9602051E-02 at 170iterations 7.9364626E-04 1.6984940E-02 at 180iterations finished qdiffx linear iterations at : 20:16:34 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 7.9364626E-04 1.6984940E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 20:16:35 13.147u 0.227s 0:13.89 96.1% 0+0k 0+0io 0pf+0w