Mon Oct 10 14:00:53 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 14:00:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7052438 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 0.7052438 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000018 assigned positive charge : 332.2886 centred at (gu) : 90.07607 90.70670 90.94127 assigned negative charge : -325.2889 centred at (gu) : 89.98354 90.78441 91.06050 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7441 nv = 96 ne = 84 npr = 45362 no. pairs analyzed = 45362 no. exposed pairs = 2969 no. arc points = 20810 no. surface atoms = 998 nbur = 1216 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 535 mr = 3927 m= 8 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1891 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8315 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5626170E-08 -3.4155370E-09 midg,1,midg; midg,igrid,midg 8.2705903E-08 2.0865667E-08 1,midg,midg; igrid,midg,midg 1.1065030E-08 1.0340827E-07 gauss-seidel spectral radius is 0.9895414 estimated iterations to convergence 80 setup time was (sec) 0.5500000 now iterating at: 14:00:53 rms-change max change #iterations 0.2009329 29.92804 at 10iterations 2.4423035E-02 3.489639 at 20iterations 2.9836814E-03 0.4316235 at 30iterations 3.7220371E-04 4.9684525E-02 at 40iterations 4.5918663E-05 6.7272186E-03 at 50iterations finished qdiffx linear iterations at : 14:00:57 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 4.5918663E-05 6.7272186E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 14:00:59 4.347u 0.241s 0:06.09 75.2% 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 Mon Oct 10 2011 at 14:00:59 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.115731 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 2.115731 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000018 assigned positive charge : 332.2886 centred at (gu) : 90.22825 92.11999 92.82391 assigned negative charge : -325.2889 centred at (gu) : 89.95059 92.35317 93.18138 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20810 grid for indexing accessible points = 1.400000 m= 30660 mr = 52225 m= 6395 mr = 22674 m= 679 mr = 4187 m= 20 mr = 313 m= 0 mr = 1 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.6100000 number of dielectric boundary points 36283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 16513 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) : 0.7052438 object centre at (A) : 7.050000 5.970500 15.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5552078E-02 7.6794368E-03 midg,1,midg; midg,igrid,midg 3.0952586E-02 2.0280292E-02 1,midg,midg; igrid,midg,midg -3.0712422E-03 5.4388564E-02 gauss-seidel spectral radius is 0.9988490 estimated iterations to convergence 233 setup time was (sec) 0.9500000 now iterating at: 14:01:00 rms-change max change #iterations 4.702905 250.6231 at 10iterations 2.327287 88.61362 at 20iterations 1.155772 35.88510 at 30iterations 0.5755098 20.24984 at 40iterations 0.2863630 8.267410 at 50iterations 0.1428327 4.274827 at 60iterations 7.0952900E-02 2.125317 at 70iterations 3.5320017E-02 1.074943 at 80iterations 1.7532703E-02 0.5380859 at 90iterations 8.7185716E-03 0.2490321 at 100iterations 4.3516159E-03 0.1196105 at 110iterations 2.1669343E-03 6.2845230E-02 at 120iterations finished qdiffx linear iterations at : 14:01:09 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 2.1669343E-03 6.2845230E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 14:01:10 10.028u 0.287s 0:11.07 93.0% 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 14:01:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.173597 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 3.173597 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000018 assigned positive charge : 332.2886 centred at (gu) : 90.34227 93.17990 94.23572 assigned negative charge : -325.2889 centred at (gu) : 89.92587 93.52965 94.77201 start vw surface at 0.1600000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 179421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20810 grid for indexing accessible points = 1.400000 m= 93867 mr = 126443 m= 39380 mr = 76326 m= 12193 mr = 31943 m= 2644 mr = 9286 m= 343 mr = 1906 m= 13 mr = 219 m= 0 mr = 1 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 400 time to turn everything in is 2.070000 number of dielectric boundary points 81737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 16616 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) : 2.115731 object centre at (A) : 7.050000 5.970500 15.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6279445 1.2524983E-02 midg,1,midg; midg,igrid,midg 0.1739185 0.2604784 1,midg,midg; igrid,midg,midg -3.3790241E-03 0.4165587 gauss-seidel spectral radius is 0.9993010 estimated iterations to convergence 298 setup time was (sec) 2.430000 now iterating at: 14:01:13 rms-change max change #iterations 10.53127 377.6277 at 10iterations 6.158195 136.3534 at 20iterations 3.599318 65.34583 at 30iterations 2.103600 39.56236 at 40iterations 1.229788 21.81567 at 50iterations 0.7185906 14.27675 at 60iterations 0.4199688 7.686845 at 70iterations 0.2444550 4.335625 at 80iterations 0.1430566 2.366093 at 90iterations 8.3425730E-02 1.381107 at 100iterations 4.8543233E-02 0.8251724 at 110iterations 2.8307255E-02 0.4577289 at 120iterations 1.6503530E-02 0.2832451 at 130iterations 9.6263709E-03 0.1628790 at 140iterations 5.6082918E-03 9.3550205E-02 at 150iterations 3.2726144E-03 5.8887482E-02 at 160iterations 1.9100126E-03 3.0920982E-02 at 170iterations 1.1223082E-03 2.0233154E-02 at 180iterations finished qdiffx linear iterations at : 14:01:27 total time elapsed so far: 16.32000 # loops : 180 mean,max change (kT/e) : 1.1223082E-03 2.0233154E-02 energy calculations done at 16.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.51000 DelPhi exited at 14:01:28 16.513u 0.333s 0:17.22 97.7% 0+0k 0+0io 0pf+0w