Sat Oct 8 11:37:31 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 Sat Oct 8 2011 at 11:37:31 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4120 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 0.5805326 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): -25.63000 35.69300 ymin,ymax (A): 39.93800 97.43200 zmin,zma (A): 31.67600 89.72900 x,y,z range (A): 61.32300 57.49400 58.05299 scale (grids/A): 0.5805326 object centre (A): 5.031501 68.68500 60.70250 number of atom coordinates read : 4120 total number of charged atoms : 3961 net assigned charge : -4.485940 assigned positive charge : 612.6949 centred at (gu) : 90.36993 88.67227 88.84172 assigned negative charge : -617.1835 centred at (gu) : 90.21947 88.76983 89.00948 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9132 nv = 96 ne = 84 npr = 85860 no. pairs analyzed = 85860 no. exposed pairs = 4778 no. arc points = 31864 no. surface atoms = 1628 nbur = 2492 mkacc time = 0.1400000 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 = 1.512000 m= 452 mr = 5333 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2900000 number of dielectric boundary points 4205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3327 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 11731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2799591E-09 -4.8977009E-09 midg,1,midg; midg,igrid,midg 2.6007188E-09 -3.0656611E-09 1,midg,midg; igrid,midg,midg -5.3812053E-09 3.7941676E-09 gauss-seidel spectral radius is 0.9847692 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 11:37:31 rms-change max change #iterations 0.1207776 16.28305 at 10iterations 9.9448506E-03 1.348640 at 20iterations 1.2536080E-03 0.1573486 at 30iterations 3.4566122E-04 4.1175783E-02 at 40iterations 1.2471329E-04 1.6293943E-02 at 50iterations finished qdiffx linear iterations at : 11:37:35 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.2471329E-04 1.6293943E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:37:35 3.895u 0.235s 0:04.65 88.6% 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 11:37:35 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4120 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 1.741598 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): -25.63000 35.69300 ymin,ymax (A): 39.93800 97.43200 zmin,zma (A): 31.67600 89.72900 x,y,z range (A): 61.32300 57.49400 58.05299 scale (grids/A): 1.741598 object centre (A): 5.031501 68.68500 60.70250 number of atom coordinates read : 4120 total number of charged atoms : 3961 net assigned charge : -4.485940 assigned positive charge : 612.6949 centred at (gu) : 91.10817 86.01559 86.52387 assigned negative charge : -617.1835 centred at (gu) : 90.65779 86.30909 87.02794 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 100462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31864 grid for indexing accessible points = 1.400000 m= 37466 mr = 73015 m= 5614 mr = 28253 m= 224 mr = 3531 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4717 time to turn everything in is 0.4900000 number of dielectric boundary points 38912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 30786 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) : 0.5805326 object centre at (A) : 5.031501 68.68500 60.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7885217E-02 -3.1115180E-02 midg,1,midg; midg,igrid,midg 2.4794370E-02 -6.6903550E-03 1,midg,midg; igrid,midg,midg -2.5406377E-02 3.2150298E-02 gauss-seidel spectral radius is 0.9985140 estimated iterations to convergence 206 setup time was (sec) 0.7200000 now iterating at: 11:37:36 rms-change max change #iterations 4.606479 175.1278 at 10iterations 2.092046 62.11559 at 20iterations 0.9477924 27.29566 at 30iterations 0.4294061 13.28727 at 40iterations 0.1955719 5.310338 at 50iterations 8.8622220E-02 2.953859 at 60iterations 4.0472750E-02 1.233505 at 70iterations 1.8536970E-02 0.5069337 at 80iterations 8.5356897E-03 0.2733421 at 90iterations 4.0181475E-03 0.1161728 at 100iterations 1.9582890E-03 6.0574055E-02 at 110iterations 1.0129550E-03 2.9891968E-02 at 120iterations finished qdiffx linear iterations at : 11:37:58 total time elapsed so far: 8.480000 # loops : 120 mean,max change (kT/e) : 1.0129550E-03 2.9891968E-02 energy calculations done at 8.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 11:37:59 8.613u 0.232s 0:23.76 37.2% 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 Sat Oct 8 2011 at 11:37:59 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4120 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 2.612397 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): -25.63000 35.69300 ymin,ymax (A): 39.93800 97.43200 zmin,zma (A): 31.67600 89.72900 x,y,z range (A): 61.32300 57.49400 58.05299 scale (grids/A): 2.612397 object centre (A): 5.031501 68.68500 60.70250 number of atom coordinates read : 4120 total number of charged atoms : 3961 net assigned charge : -4.485940 assigned positive charge : 612.6949 centred at (gu) : 91.66192 84.02312 84.78566 assigned negative charge : -617.1835 centred at (gu) : 90.98653 84.46352 85.54179 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 232585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31864 grid for indexing accessible points = 1.400000 m= 122186 mr = 176324 m= 43931 mr = 101502 m= 9912 mr = 35687 m= 1146 mr = 7580 m= 28 mr = 758 m= 0 mr = 5 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 15608 time to turn everything in is 1.290000 number of dielectric boundary points 87932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 31680 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) : 1.741598 object centre at (A) : 5.031501 68.68500 60.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8651733 -0.3653329 midg,1,midg; midg,igrid,midg 0.3621756 4.0154759E-02 1,midg,midg; igrid,midg,midg -0.3294724 0.3237413 gauss-seidel spectral radius is 0.9992508 estimated iterations to convergence 288 setup time was (sec) 1.570000 now iterating at: 11:38:01 rms-change max change #iterations 11.31361 258.3463 at 10iterations 6.630580 136.3742 at 20iterations 3.862691 74.14157 at 30iterations 2.244513 38.04977 at 40iterations 1.299124 21.79601 at 50iterations 0.7491115 12.68998 at 60iterations 0.4327794 7.347244 at 70iterations 0.2493346 4.924433 at 80iterations 0.1434755 2.329497 at 90iterations 8.2515873E-02 1.586498 at 100iterations 4.7580946E-02 0.8287499 at 110iterations 2.7410666E-02 0.4397926 at 120iterations 1.5811881E-02 0.2549648 at 130iterations 9.1951014E-03 0.1511436 at 140iterations 5.4141409E-03 8.3643198E-02 at 150iterations 3.2555899E-03 5.6833267E-02 at 160iterations 2.0157911E-03 3.2875538E-02 at 170iterations 1.3112021E-03 2.3979187E-02 at 180iterations finished qdiffx linear iterations at : 11:38:14 total time elapsed so far: 14.26000 # loops : 180 mean,max change (kT/e) : 1.3112021E-03 2.3979187E-02 energy calculations done at 14.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 11:38:14 14.388u 0.257s 0:15.16 96.5% 0+0k 0+0io 0pf+0w