Sun Oct 9 00:05:50 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 Sun Oct 9 2011 at 00:05:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2435 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: 0.6269703 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): 82.85201 125.0510 ymin,ymax (A): 67.15600 120.5920 zmin,zma (A): 54.03800 110.8190 x,y,z range (A): 42.19900 53.43600 56.78100 scale (grids/A): 0.6269703 object centre (A): 103.9515 93.87400 82.42850 number of atom coordinates read : 2435 total number of charged atoms : 2298 net assigned charge : 9.000029 assigned positive charge : 356.7652 centred at (gu) : 90.50516 89.10551 89.40527 assigned negative charge : -347.7660 centred at (gu) : 90.36459 89.14204 89.49271 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6549 nv = 96 ne = 84 npr = 48614 no. pairs analyzed = 48614 no. exposed pairs = 3201 no. arc points = 22497 no. surface atoms = 1076 nbur = 1359 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3430 m= 0 mr = 30 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3200000 number of dielectric boundary points 3460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2292 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7187851E-08 2.1573834E-09 midg,1,midg; midg,igrid,midg 1.3885783E-08 5.1245146E-09 1,midg,midg; igrid,midg,midg -1.3502307E-09 2.1072683E-08 gauss-seidel spectral radius is 0.9868165 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 00:05:51 rms-change max change #iterations 0.1242170 19.45224 at 10iterations 1.1878800E-02 1.895384 at 20iterations 1.4403590E-03 0.2143660 at 30iterations 3.7260208E-04 5.8792114E-02 at 40iterations 1.3621387E-04 2.1617889E-02 at 50iterations finished qdiffx linear iterations at : 00:05:55 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.3621387E-04 2.1617889E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 00:05:55 4.201u 0.276s 0:04.73 94.5% 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 Sun Oct 9 2011 at 00:05:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2435 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: 1.880911 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): 82.85201 125.0510 ymin,ymax (A): 67.15600 120.5920 zmin,zma (A): 54.03800 110.8190 x,y,z range (A): 42.19900 53.43600 56.78100 scale (grids/A): 1.880911 object centre (A): 103.9515 93.87400 82.42850 number of atom coordinates read : 2435 total number of charged atoms : 2298 net assigned charge : 9.000029 assigned positive charge : 356.7652 centred at (gu) : 91.51515 87.31583 88.21541 assigned negative charge : -347.7660 centred at (gu) : 91.09371 87.42573 88.47792 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22497 grid for indexing accessible points = 1.400000 m= 25674 mr = 47307 m= 4355 mr = 18528 m= 251 mr = 2731 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 31626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18054 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) : 0.6269703 object centre at (A) : 103.9515 93.87400 82.42850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2777316E-02 -5.8992775E-03 midg,1,midg; midg,igrid,midg 2.3799354E-02 3.6000725E-02 1,midg,midg; igrid,midg,midg -2.4930725E-03 2.8541742E-02 gauss-seidel spectral radius is 0.9985944 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 00:05:56 rms-change max change #iterations 3.893270 167.6778 at 10iterations 1.792075 67.10237 at 20iterations 0.8299055 28.11360 at 30iterations 0.3855845 13.22255 at 40iterations 0.1780311 6.082251 at 50iterations 8.2609244E-02 2.579358 at 60iterations 3.8264796E-02 1.311966 at 70iterations 1.7782366E-02 0.6562958 at 80iterations 8.3211558E-03 0.2916856 at 90iterations 3.9600590E-03 0.1248703 at 100iterations 1.9369320E-03 7.2284698E-02 at 110iterations 9.9978712E-04 3.4278870E-02 at 120iterations finished qdiffx linear iterations at : 00:06:05 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 9.9978712E-04 3.4278870E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 00:06:06 9.792u 0.357s 0:10.48 96.7% 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 Sun Oct 9 2011 at 00:06:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2435 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: 2.821366 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): 82.85201 125.0510 ymin,ymax (A): 67.15600 120.5920 zmin,zma (A): 54.03800 110.8190 x,y,z range (A): 42.19900 53.43600 56.78100 scale (grids/A): 2.821366 object centre (A): 103.9515 93.87400 82.42850 number of atom coordinates read : 2435 total number of charged atoms : 2298 net assigned charge : 9.000029 assigned positive charge : 356.7652 centred at (gu) : 92.27261 85.97365 87.32301 assigned negative charge : -347.7660 centred at (gu) : 91.64064 86.13866 87.71692 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 161852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22497 grid for indexing accessible points = 1.400000 m= 81621 mr = 115202 m= 30787 mr = 65699 m= 7850 mr = 24486 m= 1168 mr = 5921 m= 77 mr = 770 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 71239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 18378 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) : 1.880911 object centre at (A) : 103.9515 93.87400 82.42850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5490938 -0.4925860 midg,1,midg; midg,igrid,midg 0.2601376 0.4874026 1,midg,midg; igrid,midg,midg -2.2081528E-02 0.2917736 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 2.000000 now iterating at: 00:06:08 rms-change max change #iterations 9.337979 304.3934 at 10iterations 5.487069 129.9021 at 20iterations 3.200169 74.64474 at 30iterations 1.865575 45.91125 at 40iterations 1.083178 26.67444 at 50iterations 0.6261463 12.16249 at 60iterations 0.3623956 8.332880 at 70iterations 0.2092207 4.097584 at 80iterations 0.1204458 2.439781 at 90iterations 6.9609925E-02 1.371456 at 100iterations 4.0011637E-02 0.7945213 at 110iterations 2.3061151E-02 0.4331207 at 120iterations 1.3306556E-02 0.2670774 at 130iterations 7.6835542E-03 0.1423683 at 140iterations 4.4543464E-03 8.0900192E-02 at 150iterations 2.6001998E-03 5.3822041E-02 at 160iterations 1.5401224E-03 3.2602310E-02 at 170iterations 9.3745202E-04 2.1438360E-02 at 180iterations finished qdiffx linear iterations at : 00:06:22 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 9.3745202E-04 2.1438360E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.63000 DelPhi exited at 00:06:23 16.629u 0.329s 0:17.22 98.3% 0+0k 0+0io 0pf+0w