Tue Oct 11 07:29:05 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 Tue Oct 11 2011 at 07:29:05 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 = 3262 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5934718 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 0.5934718 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4000088 assigned positive charge : 490.3148 centred at (gu) : 89.25549 89.47237 90.78075 assigned negative charge : -489.9160 centred at (gu) : 89.18747 89.38963 90.71894 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7586 nv = 96 ne = 84 npr = 67109 no. pairs analyzed = 67109 no. exposed pairs = 3857 no. arc points = 25732 no. surface atoms = 1321 nbur = 1941 mkacc time = 0.1200000 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 = 1.456000 m= 362 mr = 4380 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9522 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8122892E-09 2.9548151E-09 midg,1,midg; midg,igrid,midg -3.3650160E-09 2.8603346E-09 1,midg,midg; igrid,midg,midg -2.8727676E-09 2.2642799E-09 gauss-seidel spectral radius is 0.9853557 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 07:29:06 rms-change max change #iterations 0.1173955 17.54221 at 10iterations 1.1139395E-02 1.815178 at 20iterations 1.5778795E-03 0.2358723 at 30iterations 4.0812837E-04 6.6041946E-02 at 40iterations 1.2041064E-04 1.9266129E-02 at 50iterations finished qdiffx linear iterations at : 07:29:09 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.2041064E-04 1.9266129E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 07:29:09 3.481u 0.183s 0:04.26 85.9% 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 Oct 11 2011 at 07:29:09 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 = 3262 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.780416 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 1.780416 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4000088 assigned positive charge : 490.3148 centred at (gu) : 87.76569 88.41628 92.34110 assigned negative charge : -489.9160 centred at (gu) : 87.56216 88.16871 92.15644 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25732 grid for indexing accessible points = 1.400000 m= 30312 mr = 59737 m= 4112 mr = 22910 m= 147 mr = 2496 m= 0 mr = 33 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 766 time to turn everything in is 0.4100000 number of dielectric boundary points 32286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 24256 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) : 0.5934718 object centre at (A) : 25.55900 20.48350 30.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3895766E-02 1.1849189E-02 midg,1,midg; midg,igrid,midg -1.8382838E-02 8.4476359E-03 1,midg,midg; igrid,midg,midg 4.4309762E-03 1.3891098E-02 gauss-seidel spectral radius is 0.9985020 estimated iterations to convergence 205 setup time was (sec) 0.6300000 now iterating at: 07:29:10 rms-change max change #iterations 4.235782 193.1961 at 10iterations 1.914297 65.71014 at 20iterations 0.8690484 26.81942 at 30iterations 0.3909474 12.23222 at 40iterations 0.1776290 5.419502 at 50iterations 8.1032522E-02 2.463205 at 60iterations 3.6877714E-02 1.247566 at 70iterations 1.6847624E-02 0.5119700 at 80iterations 7.8175003E-03 0.2418175 at 90iterations 3.7413028E-03 0.1194820 at 100iterations 1.8421195E-03 6.3949585E-02 at 110iterations 9.5395348E-04 3.5926819E-02 at 120iterations finished qdiffx linear iterations at : 07:29:18 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 9.5395348E-04 3.5926819E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 07:29:18 8.023u 0.212s 0:08.72 94.3% 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 Oct 11 2011 at 07:29:18 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 = 3262 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.670623 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 2.670623 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4000088 assigned positive charge : 490.3148 centred at (gu) : 86.64812 87.62404 93.51148 assigned negative charge : -489.9160 centred at (gu) : 86.34315 87.25289 93.23459 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 192031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25732 grid for indexing accessible points = 1.400000 m= 99874 mr = 144489 m= 34343 mr = 83077 m= 6987 mr = 27998 m= 613 mr = 5196 m= 15 mr = 340 m= 0 mr = 3 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2447 time to turn everything in is 1.080000 number of dielectric boundary points 72760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 24870 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) : 1.780416 object centre at (A) : 25.55900 20.48350 30.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3490008 0.1115074 midg,1,midg; midg,igrid,midg -0.3519204 0.1163946 1,midg,midg; igrid,midg,midg 0.1311047 0.1641839 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.320000 now iterating at: 07:29:20 rms-change max change #iterations 10.25089 284.9012 at 10iterations 5.946158 129.3845 at 20iterations 3.421851 71.83102 at 30iterations 1.961316 34.67653 at 40iterations 1.122443 19.98792 at 50iterations 0.6427671 12.35494 at 60iterations 0.3677797 6.416887 at 70iterations 0.2098900 3.741325 at 80iterations 0.1198243 2.059864 at 90iterations 6.8255998E-02 1.290150 at 100iterations 3.8917702E-02 0.6776123 at 110iterations 2.2204779E-02 0.3912659 at 120iterations 1.2703498E-02 0.2239113 at 130iterations 7.3236898E-03 0.1309490 at 140iterations 4.2570694E-03 8.7810516E-02 at 150iterations 2.5214469E-03 4.5415878E-02 at 160iterations 1.5318859E-03 2.9741287E-02 at 170iterations 9.6811622E-04 1.8051147E-02 at 180iterations finished qdiffx linear iterations at : 07:29:31 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 9.6811622E-04 1.8051147E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 07:29:32 13.013u 0.200s 0:13.72 96.2% 0+0k 0+0io 0pf+0w