Tue Oct 11 06:28:40 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+sph2.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 = amb2.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 06:28:40 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6853666 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 0.6853666 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1914 net assigned charge : 6.931010 assigned positive charge : 310.7091 centred at (gu) : 88.77673 89.88954 90.58765 assigned negative charge : -303.7782 centred at (gu) : 88.70854 90.06179 90.59380 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6376 nv = 96 ne = 84 npr = 41388 no. pairs analyzed = 41388 no. exposed pairs = 2481 no. arc points = 16893 no. surface atoms = 845 nbur = 1203 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3593 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2253304E-08 3.6515459E-08 midg,1,midg; midg,igrid,midg 8.5159755E-08 -1.5917902E-08 1,midg,midg; igrid,midg,midg 1.8048958E-08 4.2418201E-08 gauss-seidel spectral radius is 0.9889050 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 06:28:41 rms-change max change #iterations 0.1745710 23.76019 at 10iterations 2.0429512E-02 2.916332 at 20iterations 2.5788608E-03 0.4022789 at 30iterations 3.8800301E-04 5.9967041E-02 at 40iterations 7.8287674E-05 9.2010498E-03 at 50iterations finished qdiffx linear iterations at : 06:28:43 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 7.8287674E-05 9.2010498E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:28:44 3.363u 0.164s 0:04.28 82.2% 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 Tue Oct 11 2011 at 06:28:44 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.056100 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 2.056100 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1914 net assigned charge : 6.931010 assigned positive charge : 310.7091 centred at (gu) : 86.33019 89.66848 91.76306 assigned negative charge : -303.7782 centred at (gu) : 86.12572 90.18571 91.78153 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16893 grid for indexing accessible points = 1.400000 m= 26658 mr = 48446 m= 4837 mr = 19977 m= 411 mr = 3130 m= 9 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 28674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15155 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) : 0.6853666 object centre at (A) : -6.562500 43.52050 8.231502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6138596E-02 5.5445172E-02 midg,1,midg; midg,igrid,midg 4.1657113E-02 2.5545806E-03 1,midg,midg; igrid,midg,midg 1.6504053E-02 9.8393699E-03 gauss-seidel spectral radius is 0.9987591 estimated iterations to convergence 225 setup time was (sec) 0.5700000 now iterating at: 06:28:45 rms-change max change #iterations 4.289658 171.9472 at 10iterations 2.091258 67.50161 at 20iterations 1.016296 35.70890 at 30iterations 0.4971203 16.33359 at 40iterations 0.2409444 7.801905 at 50iterations 0.1171174 3.694353 at 60iterations 5.7260312E-02 1.920298 at 70iterations 2.7890407E-02 0.9308014 at 80iterations 1.3685789E-02 0.4493656 at 90iterations 6.6871434E-03 0.2216454 at 100iterations 3.3108424E-03 0.1111794 at 110iterations 1.6640341E-03 6.0588837E-02 at 120iterations finished qdiffx linear iterations at : 06:28:52 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.6640341E-03 6.0588837E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 06:28:53 7.729u 0.186s 0:08.50 92.9% 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 06:28:53 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.084150 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 3.084150 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1914 net assigned charge : 6.931010 assigned positive charge : 310.7091 centred at (gu) : 84.49523 89.50283 92.64455 assigned negative charge : -303.7782 centred at (gu) : 84.18855 90.27849 92.67233 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 157949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16893 grid for indexing accessible points = 1.400000 m= 84476 mr = 116661 m= 32793 mr = 69919 m= 9003 mr = 26591 m= 1692 mr = 6917 m= 164 mr = 1151 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 64738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 15312 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) : 2.056100 object centre at (A) : -6.562500 43.52050 8.231502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3412293 0.5278343 midg,1,midg; midg,igrid,midg 0.3308761 2.3683535E-02 1,midg,midg; igrid,midg,midg 0.2174427 5.8524761E-02 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.270000 now iterating at: 06:28:54 rms-change max change #iterations 9.697128 497.3900 at 10iterations 5.688156 130.1054 at 20iterations 3.339244 65.80513 at 30iterations 1.959067 46.08704 at 40iterations 1.142506 22.70185 at 50iterations 0.6661293 12.10273 at 60iterations 0.3873765 8.515718 at 70iterations 0.2261412 4.299825 at 80iterations 0.1313369 2.536250 at 90iterations 7.6518662E-02 1.450756 at 100iterations 4.4539981E-02 0.8619003 at 110iterations 2.6068449E-02 0.4687805 at 120iterations 1.5318532E-02 0.3007240 at 130iterations 9.0994518E-03 0.1781921 at 140iterations 5.4950025E-03 9.9529266E-02 at 150iterations 3.4242403E-03 6.7466736E-02 at 160iterations 2.2340338E-03 4.1778564E-02 at 170iterations 1.5358482E-03 3.0471802E-02 at 180iterations finished qdiffx linear iterations at : 06:29:06 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 1.5358482E-03 3.0471802E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 06:29:06 12.604u 0.205s 0:13.11 97.6% 0+0k 0+0io 0pf+0w