Sat Oct 8 13:42:00 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 Sat Oct 8 2011 at 13:42:01 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 = 3015 !!! WARNING: NAP 318 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6398504 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 0.6398504 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 8.1211329E-06 assigned positive charge : 450.3736 centred at (gu) : 88.81231 89.66843 91.95625 assigned negative charge : -450.3744 centred at (gu) : 88.78860 89.56206 91.90429 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8237 nv = 96 ne = 84 npr = 62891 no. pairs analyzed = 62891 no. exposed pairs = 3485 no. arc points = 23948 no. surface atoms = 1195 nbur = 1820 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 4806 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6242774E-09 1.0597675E-08 midg,1,midg; midg,igrid,midg -1.5563947E-08 1.3069073E-08 1,midg,midg; igrid,midg,midg -4.1985388E-09 2.4131666E-09 gauss-seidel spectral radius is 0.9873764 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 13:42:01 rms-change max change #iterations 0.1609861 22.27222 at 10iterations 1.6005399E-02 2.119732 at 20iterations 1.8231632E-03 0.3027115 at 30iterations 2.8804998E-04 3.8516998E-02 at 40iterations 6.5715751E-05 9.6797943E-03 at 50iterations finished qdiffx linear iterations at : 13:42:04 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.5715751E-05 9.6797943E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:42:04 3.107u 0.166s 0:03.55 91.8% 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 Sat Oct 8 2011 at 13:42:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3015 !!! WARNING: NAP 318 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.919551 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 1.919551 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 8.1211329E-06 assigned positive charge : 450.3736 centred at (gu) : 86.43661 89.00465 95.86815 assigned negative charge : -450.3744 centred at (gu) : 86.36538 88.68592 95.71252 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23948 grid for indexing accessible points = 1.400000 m= 33622 mr = 64831 m= 5326 mr = 25458 m= 297 mr = 3372 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 35206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22598 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) : 0.6398504 object centre at (A) : 15.78000 9.4995499E-03 19.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5226524E-02 1.1925600E-02 midg,1,midg; midg,igrid,midg -3.1255099E-03 1.7351693E-02 1,midg,midg; igrid,midg,midg -9.6754720E-03 2.2556372E-02 gauss-seidel spectral radius is 0.9986876 estimated iterations to convergence 219 setup time was (sec) 0.8800000 now iterating at: 13:42:05 rms-change max change #iterations 4.691654 180.7590 at 10iterations 2.247107 69.57866 at 20iterations 1.068323 36.32822 at 30iterations 0.5094537 14.96001 at 40iterations 0.2421627 7.049164 at 50iterations 0.1156002 3.089531 at 60iterations 5.5088360E-02 1.632748 at 70iterations 2.6277572E-02 0.7811852 at 80iterations 1.2570649E-02 0.3734902 at 90iterations 6.0303188E-03 0.1872215 at 100iterations 2.9062622E-03 8.2405090E-02 at 110iterations 1.4084734E-03 4.1654587E-02 at 120iterations finished qdiffx linear iterations at : 13:42:11 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 1.4084734E-03 4.1654587E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 13:42:12 7.151u 0.180s 0:07.62 96.1% 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 Sat Oct 8 2011 at 13:42:12 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 = 3015 !!! WARNING: NAP 318 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.879327 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): -12.03900 43.59900 ymin,ymax (A): -22.28000 22.29900 zmin,zma (A): -7.897000 47.15300 x,y,z range (A): 55.63800 44.57900 55.05000 scale (grids/A): 2.879327 object centre (A): 15.78000 9.4995499E-03 19.62800 number of atom coordinates read : 3015 total number of charged atoms : 2869 net assigned charge : 8.1211329E-06 assigned positive charge : 450.3736 centred at (gu) : 84.65479 88.50673 98.80215 assigned negative charge : -450.3744 centred at (gu) : 84.54798 88.02881 98.56873 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23948 grid for indexing accessible points = 1.400000 m= 108670 mr = 156762 m= 40203 mr = 90620 m= 9482 mr = 32665 m= 1302 mr = 7065 m= 59 mr = 850 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 79421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 22949 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) : 1.919551 object centre at (A) : 15.78000 9.4995499E-03 19.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1273463 0.2085252 midg,1,midg; midg,igrid,midg 5.7898792E-03 0.1899057 1,midg,midg; igrid,midg,midg 0.1154324 0.3409294 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.850000 now iterating at: 13:42:14 rms-change max change #iterations 10.96229 416.2627 at 10iterations 6.453835 165.8309 at 20iterations 3.779954 71.88994 at 30iterations 2.212542 38.62036 at 40iterations 1.286387 21.61509 at 50iterations 0.7491579 12.12876 at 60iterations 0.4354633 7.837185 at 70iterations 0.2527003 4.149749 at 80iterations 0.1470380 2.558913 at 90iterations 8.5195929E-02 1.413742 at 100iterations 4.9522474E-02 0.8630791 at 110iterations 2.8619621E-02 0.4570160 at 120iterations 1.6671794E-02 0.3028221 at 130iterations 9.6713090E-03 0.1598816 at 140iterations 5.6334203E-03 9.2522144E-02 at 150iterations 3.2941550E-03 5.6114197E-02 at 160iterations 1.9402511E-03 3.3769608E-02 at 170iterations 1.1553614E-03 1.9347191E-02 at 180iterations finished qdiffx linear iterations at : 13:42:23 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 1.1553614E-03 1.9347191E-02 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 13:42:24 11.695u 0.200s 0:12.18 97.6% 0+0k 0+0io 0pf+0w