Tue Oct 11 03:14:27 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 03:14:27 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 0.6016156 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 0.6016156 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.400021 assigned positive charge : 438.4451 centred at (gu) : 89.75130 93.14429 89.62594 assigned negative charge : -435.0464 centred at (gu) : 89.76531 93.20896 89.57381 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7176 nv = 96 ne = 84 npr = 57541 no. pairs analyzed = 57541 no. exposed pairs = 4114 no. arc points = 29123 no. surface atoms = 1347 nbur = 1567 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 337 mr = 3490 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2200000 number of dielectric boundary points 4010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2915 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6549150E-10 3.5137118E-09 midg,1,midg; midg,igrid,midg 2.1617690E-09 -2.5168017E-09 1,midg,midg; igrid,midg,midg 2.3433322E-09 9.7397979E-10 gauss-seidel spectral radius is 0.9857397 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 03:14:28 rms-change max change #iterations 0.1159994 18.57276 at 10iterations 1.0275432E-02 1.622068 at 20iterations 1.3630805E-03 0.2090263 at 30iterations 3.9295160E-04 6.4966202E-02 at 40iterations 1.3980092E-04 2.3252487E-02 at 50iterations finished qdiffx linear iterations at : 03:14:31 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.3980092E-04 2.3252487E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:14:31 3.442u 0.158s 0:04.17 86.0% 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 03:14:31 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 1.804847 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 1.804847 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.400021 assigned positive charge : 438.4451 centred at (gu) : 89.25300 99.43205 88.87724 assigned negative charge : -435.0464 centred at (gu) : 89.29562 99.62680 88.72108 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29123 grid for indexing accessible points = 1.400000 m= 25464 mr = 50759 m= 3291 mr = 16959 m= 149 mr = 1584 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3900000 number of dielectric boundary points 37227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21708 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) : 0.6016156 object centre at (A) : -0.6485004 -8.506999 2.887000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5314154E-02 6.2599862E-03 midg,1,midg; midg,igrid,midg -4.5466307E-03 -1.3201824E-02 1,midg,midg; igrid,midg,midg 2.8805388E-02 -4.5042648E-03 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 0.6100000 now iterating at: 03:14:32 rms-change max change #iterations 4.096311 183.7933 at 10iterations 1.861094 68.81331 at 20iterations 0.8509662 30.29187 at 30iterations 0.3876391 12.49641 at 40iterations 0.1775304 6.215523 at 50iterations 8.1072129E-02 2.472277 at 60iterations 3.7242908E-02 1.221802 at 70iterations 1.7024675E-02 0.6237450 at 80iterations 7.8751938E-03 0.2585182 at 90iterations 3.7047814E-03 0.1261597 at 100iterations 1.7940615E-03 6.7523956E-02 at 110iterations 9.1283716E-04 3.1338692E-02 at 120iterations finished qdiffx linear iterations at : 03:14:39 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 9.1283716E-04 3.1338692E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 03:14:40 7.867u 0.199s 0:08.43 95.4% 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 03:14:40 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 2.707270 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): -26.43300 25.13600 ymin,ymax (A): -38.09400 21.08000 zmin,zma (A): -23.80100 29.57500 x,y,z range (A): 51.56900 59.17400 53.37600 scale (grids/A): 2.707270 object centre (A): -0.6485004 -8.506999 2.887000 number of atom coordinates read : 2914 total number of charged atoms : 2783 net assigned charge : 3.400021 assigned positive charge : 438.4451 centred at (gu) : 88.87939 104.1481 88.31567 assigned negative charge : -435.0464 centred at (gu) : 88.94349 104.4403 88.08154 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29123 grid for indexing accessible points = 1.400000 m= 83723 mr = 124655 m= 27563 mr = 64608 m= 5479 mr = 20359 m= 529 mr = 3488 m= 20 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.9700000 number of dielectric boundary points 83880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 22263 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) : 1.804847 object centre at (A) : -0.6485004 -8.506999 2.887000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2532623 8.8280797E-02 midg,1,midg; midg,igrid,midg -0.1543385 -0.2803056 1,midg,midg; igrid,midg,midg 0.3658725 -8.0034629E-02 gauss-seidel spectral radius is 0.9992652 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 03:14:42 rms-change max change #iterations 10.15403 369.6997 at 10iterations 6.060775 158.7148 at 20iterations 3.591007 95.18359 at 30iterations 2.115978 58.20328 at 40iterations 1.240035 30.06454 at 50iterations 0.7245272 17.97897 at 60iterations 0.4217658 8.788019 at 70iterations 0.2447497 5.186378 at 80iterations 0.1422316 2.930998 at 90iterations 8.2317434E-02 1.791016 at 100iterations 4.7759142E-02 0.9947977 at 110iterations 2.7629618E-02 0.5435371 at 120iterations 1.5976124E-02 0.3432465 at 130iterations 9.2442511E-03 0.1825104 at 140iterations 5.3680530E-03 0.1021039 at 150iterations 3.1206100E-03 6.6452026E-02 at 160iterations 1.8285019E-03 3.8528442E-02 at 170iterations 1.0870533E-03 2.2560120E-02 at 180iterations finished qdiffx linear iterations at : 03:14:53 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.0870533E-03 2.2560120E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 03:14:54 12.842u 0.212s 0:13.33 97.8% 0+0k 0+0io 0pf+0w