Wed Feb 15 08:54:35 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HID 69 has a net charge of 1.4000 !!! WARNING: HID 84 has a net charge of 1.4000 !!! WARNING: HIE 97 has a net charge of 1.4000 !!! WARNING: HID 119 has a net charge of 1.4000 !!! WARNING: HID 123 has a net charge of 1.4000 !!! WARNING: HID 129 has a net charge of 1.4000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HID 233 has a net charge of 1.4000 !!! WARNING: HID 248 has a net charge of 1.4000 !!! WARNING: HIE 261 has a net charge of 1.4000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 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: 0.6324279 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 0.6324279 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1740 net assigned charge : 6.800021 assigned positive charge : 276.5604 centred at (gu) : 88.03694 89.78539 90.39578 assigned negative charge : -269.7603 centred at (gu) : 87.75250 89.94267 90.19516 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5245 nv = 96 ne = 84 npr = 42185 no. pairs analyzed = 42185 no. exposed pairs = 2607 no. arc points = 18797 no. surface atoms = 883 nbur = 1087 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 256 mr = 2599 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2800000 number of dielectric boundary points 2877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6683999E-09 2.3026937E-08 midg,1,midg; midg,igrid,midg 1.9281455E-08 -2.0610085E-09 1,midg,midg; igrid,midg,midg -1.7239337E-08 1.7294486E-08 gauss-seidel spectral radius is 0.9869979 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 08:54:36 rms-change max change #iterations 0.1398440 22.63416 at 10iterations 1.3359098E-02 2.238068 at 20iterations 1.2647547E-03 0.1945152 at 30iterations 1.1953792E-04 1.8430710E-02 at 40iterations 1.1494726E-05 1.8978119E-03 at 50iterations finished qdiffx linear iterations at : 08:54:38 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.1494726E-05 1.8978119E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:54:40 3.342u 0.155s 0:04.99 69.9% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:54:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HID 69 has a net charge of 1.4000 !!! WARNING: HID 84 has a net charge of 1.4000 !!! WARNING: HIE 97 has a net charge of 1.4000 !!! WARNING: HID 119 has a net charge of 1.4000 !!! WARNING: HID 123 has a net charge of 1.4000 !!! WARNING: HID 129 has a net charge of 1.4000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HID 233 has a net charge of 1.4000 !!! WARNING: HID 248 has a net charge of 1.4000 !!! WARNING: HIE 261 has a net charge of 1.4000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 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: 1.897284 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 1.897284 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1740 net assigned charge : 6.800021 assigned positive charge : 276.5604 centred at (gu) : 84.11115 89.35653 91.18754 assigned negative charge : -269.7603 centred at (gu) : 83.25764 89.82813 90.58575 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 55804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 17693 mr = 36103 m= 2363 mr = 12178 m= 121 mr = 1363 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.4500000 number of dielectric boundary points 26295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13675 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) : 0.6324279 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8856050E-02 2.0032575E-02 midg,1,midg; midg,igrid,midg 1.3191302E-02 4.6946746E-03 1,midg,midg; igrid,midg,midg 1.0582096E-02 4.3643728E-02 gauss-seidel spectral radius is 0.9985654 estimated iterations to convergence 209 setup time was (sec) 0.7300000 now iterating at: 08:54:42 rms-change max change #iterations 3.658517 184.1944 at 10iterations 1.681433 62.73542 at 20iterations 0.7707040 27.97694 at 30iterations 0.3520307 12.92788 at 40iterations 0.1620886 6.127518 at 50iterations 7.4442968E-02 2.680193 at 60iterations 3.4159716E-02 1.273003 at 70iterations 1.5629524E-02 0.5564270 at 80iterations 7.1620750E-03 0.2928238 at 90iterations 3.2942696E-03 0.1152344 at 100iterations 1.5015032E-03 5.2185059E-02 at 110iterations 6.9187197E-04 2.5955200E-02 at 120iterations finished qdiffx linear iterations at : 08:54:48 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 6.9187197E-04 2.5955200E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 08:54:49 7.394u 0.165s 0:08.19 92.1% 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 Wed Feb 15 2012 at 08:54:49 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HID 69 has a net charge of 1.4000 !!! WARNING: HID 84 has a net charge of 1.4000 !!! WARNING: HIE 97 has a net charge of 1.4000 !!! WARNING: HID 119 has a net charge of 1.4000 !!! WARNING: HID 123 has a net charge of 1.4000 !!! WARNING: HID 129 has a net charge of 1.4000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HID 233 has a net charge of 1.4000 !!! WARNING: HID 248 has a net charge of 1.4000 !!! WARNING: HIE 261 has a net charge of 1.4000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 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: 2.845926 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 2.845926 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1740 net assigned charge : 6.800021 assigned positive charge : 276.5604 centred at (gu) : 81.16677 89.03490 91.78132 assigned negative charge : -269.7603 centred at (gu) : 79.88658 89.74220 90.87857 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 129395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 58882 mr = 88622 m= 18974 mr = 45952 m= 3934 mr = 14616 m= 520 mr = 2808 m= 26 mr = 352 m= 0 mr = 4 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 1321 time to turn everything in is 1.050000 number of dielectric boundary points 59377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 13915 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) : 1.897284 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5961646 0.1578008 midg,1,midg; midg,igrid,midg 9.9287920E-02 8.0356017E-02 1,midg,midg; igrid,midg,midg -0.1710625 0.5152699 gauss-seidel spectral radius is 0.9992404 estimated iterations to convergence 286 setup time was (sec) 1.340000 now iterating at: 08:54:55 rms-change max change #iterations 8.580306 344.7257 at 10iterations 4.972044 122.0437 at 20iterations 2.861808 61.72515 at 30iterations 1.646153 49.57150 at 40iterations 0.9443426 23.86964 at 50iterations 0.5406808 11.66281 at 60iterations 0.3090290 7.416172 at 70iterations 0.1761851 3.652229 at 80iterations 0.1006756 2.148261 at 90iterations 5.7393517E-02 1.205383 at 100iterations 3.2789037E-02 0.7550964 at 110iterations 1.8647838E-02 0.4043961 at 120iterations 1.0640584E-02 0.2362223 at 130iterations 6.0562519E-03 0.1327991 at 140iterations 3.4518971E-03 6.9460154E-02 at 150iterations 1.9631840E-03 4.4189453E-02 at 160iterations 1.1178477E-03 2.1549225E-02 at 170iterations 6.3936319E-04 1.4499664E-02 at 180iterations finished qdiffx linear iterations at : 08:55:05 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 6.3936319E-04 1.4499664E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 08:55:06 11.626u 0.186s 0:16.91 69.7% 0+0k 0+0io 0pf+0w