Mon Oct 10 13:52:31 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 13:52:31 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 0.5714561 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 0.5714561 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030021 assigned positive charge : 515.3898 centred at (gu) : 90.91619 89.83347 87.81409 assigned negative charge : -512.3611 centred at (gu) : 90.83108 89.92357 87.78883 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7369 nv = 96 ne = 84 npr = 64368 no. pairs analyzed = 64368 no. exposed pairs = 4448 no. arc points = 31541 no. surface atoms = 1493 nbur = 1848 mkacc time = 0.1700000 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= 396 mr = 3763 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3068 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9176 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0275734E-11 5.7517913E-10 midg,1,midg; midg,igrid,midg 2.2534470E-09 -1.1926787E-09 1,midg,midg; igrid,midg,midg -9.1540420E-10 2.5832625E-09 gauss-seidel spectral radius is 0.9842359 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 13:52:32 rms-change max change #iterations 9.4830826E-02 13.06669 at 10iterations 7.0750634E-03 1.253799 at 20iterations 5.4119818E-04 8.4209442E-02 at 30iterations 4.2235442E-05 5.8670044E-03 at 40iterations 8.9309051E-06 1.2745857E-03 at 50iterations finished qdiffx linear iterations at : 13:52:36 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 8.9309051E-06 1.2745857E-03 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 13:52:37 4.961u 0.372s 0:05.66 94.1% 0+0k 0+0io 4pf+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 13:52:37 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 1.714368 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 1.714368 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030021 assigned positive charge : 515.3898 centred at (gu) : 92.74770 89.49965 83.44123 assigned negative charge : -512.3611 centred at (gu) : 92.49297 89.77029 83.36614 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31541 grid for indexing accessible points = 1.400000 m= 27305 mr = 54445 m= 3604 mr = 18647 m= 139 mr = 1845 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 36914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 24598 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) : 0.5714561 object centre at (A) : 19.87750 14.92700 47.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2298305E-02 5.5238828E-03 midg,1,midg; midg,igrid,midg 1.8020011E-02 -1.1308693E-02 1,midg,midg; igrid,midg,midg -7.6131364E-03 -8.9779748E-03 gauss-seidel spectral radius is 0.9984035 estimated iterations to convergence 199 setup time was (sec) 1.010000 now iterating at: 13:52:46 rms-change max change #iterations 4.047208 181.0127 at 10iterations 1.780162 71.77624 at 20iterations 0.7857267 26.92453 at 30iterations 0.3466516 11.79378 at 40iterations 0.1538291 5.035236 at 50iterations 6.7786433E-02 2.273026 at 60iterations 3.0034102E-02 0.9405575 at 70iterations 1.3210006E-02 0.4828876 at 80iterations 5.8477186E-03 0.2039404 at 90iterations 2.6053390E-03 8.5115910E-02 at 100iterations 1.1696726E-03 4.3211818E-02 at 110iterations 5.4907863E-04 1.9370079E-02 at 120iterations finished qdiffx linear iterations at : 13:52:57 total time elapsed so far: 12.17000 # loops : 120 mean,max change (kT/e) : 5.4907863E-04 1.9370079E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 13:52:58 12.340u 0.484s 0:21.65 59.2% 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 13:52:58 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.571552 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): -11.27100 51.02600 ymin,ymax (A): -12.71500 42.56900 zmin,zma (A): 19.67300 75.95800 x,y,z range (A): 62.29700 55.28400 56.28500 scale (grids/A): 2.571552 object centre (A): 19.87750 14.92700 47.81550 number of atom coordinates read : 3341 total number of charged atoms : 3184 net assigned charge : 3.030021 assigned positive charge : 515.3898 centred at (gu) : 94.12131 89.24928 80.16157 assigned negative charge : -512.3611 centred at (gu) : 93.73932 89.65542 80.04904 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 187324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31541 grid for indexing accessible points = 1.400000 m= 90586 mr = 132964 m= 29830 mr = 71396 m= 5971 mr = 22239 m= 612 mr = 4012 m= 12 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 83406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 25435 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) : 1.714368 object centre at (A) : 19.87750 14.92700 47.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2420771 6.8333723E-02 midg,1,midg; midg,igrid,midg 0.2753612 -0.1721410 1,midg,midg; igrid,midg,midg 0.1199629 -0.5674113 gauss-seidel spectral radius is 0.9992175 estimated iterations to convergence 282 setup time was (sec) 2.180000 now iterating at: 13:53:01 rms-change max change #iterations 10.39497 323.7954 at 10iterations 6.126663 138.8891 at 20iterations 3.562821 91.52670 at 30iterations 2.059002 44.69915 at 40iterations 1.184109 25.58287 at 50iterations 0.6782179 15.91587 at 60iterations 0.3889003 8.242584 at 70iterations 0.2218658 4.035413 at 80iterations 0.1262309 2.403165 at 90iterations 7.1929522E-02 1.422516 at 100iterations 4.0919166E-02 0.8002663 at 110iterations 2.3246557E-02 0.4671073 at 120iterations 1.3223503E-02 0.2599869 at 130iterations 7.5205029E-03 0.1550751 at 140iterations 4.2831032E-03 8.1610203E-02 at 150iterations 2.4572655E-03 4.7958374E-02 at 160iterations 1.4328270E-03 2.8732538E-02 at 170iterations 8.6114573E-04 1.6561031E-02 at 180iterations finished qdiffx linear iterations at : 13:53:19 total time elapsed so far: 20.01000 # loops : 180 mean,max change (kT/e) : 8.6114573E-04 1.6561031E-02 energy calculations done at 20.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.18000 DelPhi exited at 13:53:19 20.188u 0.471s 0:21.01 98.2% 0+0k 0+0io 0pf+0w