Wed Dec 21 14:21:14 PST 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 Wed Dec 21 2011 at 14:21:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6403914 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 0.6403914 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 91.06739 92.50497 90.02772 assigned negative charge : -284.0643 centred at (gu) : 91.16891 92.69248 90.01454 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5464 nv = 96 ne = 84 npr = 40355 no. pairs analyzed = 40355 no. exposed pairs = 2451 no. arc points = 17362 no. surface atoms = 827 nbur = 1126 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3049 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 2685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1663 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6253494E-10 3.2388570E-09 midg,1,midg; midg,igrid,midg 1.0421902E-08 -2.4941144E-08 1,midg,midg; igrid,midg,midg 8.4874836E-09 -8.4660723E-09 gauss-seidel spectral radius is 0.9873103 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:21:15 rms-change max change #iterations 0.1228676 20.05087 at 10iterations 1.1891690E-02 1.889874 at 20iterations 1.2041806E-03 0.1773911 at 30iterations 1.1996285E-04 2.2651672E-02 at 40iterations 1.1873702E-05 1.7361641E-03 at 50iterations finished qdiffx linear iterations at : 14:21:19 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.1873702E-05 1.7361641E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 14:21:22 4.322u 0.448s 0:07.42 64.1% 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 Dec 21 2011 at 14:21:22 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.921174 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 1.921174 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 93.20238 97.51493 90.08319 assigned negative charge : -284.0643 centred at (gu) : 93.50700 98.07745 90.04392 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 22090 mr = 40818 m= 3479 mr = 16972 m= 172 mr = 2332 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2155 time to turn everything in is 0.5600000 number of dielectric boundary points 24697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14345 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) : 0.6403914 object centre at (A) : 14.35900 22.43550 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1838776E-02 8.8675031E-03 midg,1,midg; midg,igrid,midg 3.6495540E-02 -1.7596370E-02 1,midg,midg; igrid,midg,midg 7.5208344E-03 -6.7915404E-03 gauss-seidel spectral radius is 0.9985788 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 14:21:23 rms-change max change #iterations 3.606365 166.6560 at 10iterations 1.659346 65.38206 at 20iterations 0.7709053 27.29783 at 30iterations 0.3529570 12.94137 at 40iterations 0.1633645 5.094944 at 50iterations 7.5022504E-02 2.894513 at 60iterations 3.4558624E-02 1.251577 at 70iterations 1.5935041E-02 0.5384102 at 80iterations 7.3626866E-03 0.2672272 at 90iterations 3.3978259E-03 0.1200428 at 100iterations 1.5646730E-03 5.4435253E-02 at 110iterations 7.2173547E-04 2.4971008E-02 at 120iterations finished qdiffx linear iterations at : 14:21:34 total time elapsed so far: 11.72000 # loops : 120 mean,max change (kT/e) : 7.2173547E-04 2.4971008E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 14:21:40 11.908u 0.429s 0:18.51 66.5% 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 Wed Dec 21 2011 at 14:21:41 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.881762 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): -6.098000 34.81600 ymin,ymax (A): -3.690000 48.56100 zmin,zma (A): -24.39100 31.20000 x,y,z range (A): 40.91400 52.25100 55.59100 scale (grids/A): 2.881762 object centre (A): 14.35900 22.43550 3.404501 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 285.1041 centred at (gu) : 94.80370 101.2725 90.12475 assigned negative charge : -284.0643 centred at (gu) : 95.26051 102.1162 90.06594 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 136394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 70677 mr = 98732 m= 26797 mr = 58664 m= 6346 mr = 22461 m= 740 mr = 4946 m= 41 mr = 503 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7202 time to turn everything in is 1.410000 number of dielectric boundary points 55684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14568 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) : 1.921174 object centre at (A) : 14.35900 22.43550 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.008613 -4.2533567E-03 midg,1,midg; midg,igrid,midg 0.3613910 -0.1735937 1,midg,midg; igrid,midg,midg 4.5042645E-02 -4.1986737E-02 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.840000 now iterating at: 14:21:44 rms-change max change #iterations 8.484915 372.6942 at 10iterations 4.875519 119.9408 at 20iterations 2.767462 58.46471 at 30iterations 1.572283 34.51548 at 40iterations 0.8938828 18.41834 at 50iterations 0.5077355 10.03115 at 60iterations 0.2876376 6.355895 at 70iterations 0.1630688 3.362801 at 80iterations 9.2640944E-02 1.995308 at 90iterations 5.2422669E-02 1.105232 at 100iterations 2.9752119E-02 0.6386604 at 110iterations 1.6858032E-02 0.3323135 at 120iterations 9.5730675E-03 0.1911926 at 130iterations 5.4188273E-03 0.1136780 at 140iterations 3.0667468E-03 7.5096890E-02 at 150iterations 1.7433141E-03 3.3329010E-02 at 160iterations 9.8737073E-04 1.9082069E-02 at 170iterations 5.6122948E-04 1.1470795E-02 at 180iterations finished qdiffx linear iterations at : 14:22:02 total time elapsed so far: 19.76000 # loops : 180 mean,max change (kT/e) : 5.6122948E-04 1.1470795E-02 energy calculations done at 19.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.94000 DelPhi exited at 14:22:13 19.944u 0.432s 0:32.09 63.4% 0+0k 0+0io 0pf+0w