Tue Oct 11 08:23:03 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 08:23:04 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 268 has a net charge of -0.0940 !!! WARNING: GLM 272 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6293755 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 0.6293755 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2463 net assigned charge : 4.812012 assigned positive charge : 393.3969 centred at (gu) : 89.82032 88.95617 90.07870 assigned negative charge : -388.5853 centred at (gu) : 89.92378 88.84886 90.22237 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6943 nv = 96 ne = 84 npr = 52395 no. pairs analyzed = 52395 no. exposed pairs = 3100 no. arc points = 22075 no. surface atoms = 1053 nbur = 1560 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3903 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2900000 number of dielectric boundary points 3356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7251773E-08 -7.5716944E-09 midg,1,midg; midg,igrid,midg -5.3642437E-09 1.1553710E-08 1,midg,midg; igrid,midg,midg 1.4712186E-08 -3.6819239E-09 gauss-seidel spectral radius is 0.9869249 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 08:23:04 rms-change max change #iterations 0.1401258 20.30443 at 10iterations 1.4282541E-02 2.107903 at 20iterations 2.1481977E-03 0.3954353 at 30iterations 5.6873268E-04 0.1263542 at 40iterations 1.8273303E-04 4.0981293E-02 at 50iterations finished qdiffx linear iterations at : 08:23:08 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.8273303E-04 4.0981293E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 08:23:08 4.172u 0.217s 0:04.86 90.1% 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 Tue Oct 11 2011 at 08:23:08 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 268 has a net charge of -0.0940 !!! WARNING: GLM 272 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.888127 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 1.888127 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2463 net assigned charge : 4.812012 assigned positive charge : 393.3969 centred at (gu) : 89.46057 86.86774 90.23540 assigned negative charge : -388.5853 centred at (gu) : 89.77071 86.54617 90.66687 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22075 grid for indexing accessible points = 1.400000 m= 27175 mr = 53248 m= 4055 mr = 20306 m= 204 mr = 2504 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1605 time to turn everything in is 0.5700000 number of dielectric boundary points 31025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19332 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) : 0.6293755 object centre at (A) : 24.33400 32.08400 29.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0197833E-02 7.9635661E-03 midg,1,midg; midg,igrid,midg -6.6086855E-03 2.1291137E-02 1,midg,midg; igrid,midg,midg 1.2842448E-03 -1.9168595E-02 gauss-seidel spectral radius is 0.9986116 estimated iterations to convergence 213 setup time was (sec) 0.8800000 now iterating at: 08:23:10 rms-change max change #iterations 4.236075 174.1451 at 10iterations 1.967537 74.73752 at 20iterations 0.9083544 30.02764 at 30iterations 0.4243256 12.99837 at 40iterations 0.1977777 6.754566 at 50iterations 9.2241459E-02 2.928368 at 60iterations 4.3023422E-02 1.351742 at 70iterations 2.0171089E-02 0.6319122 at 80iterations 9.6759843E-03 0.3379364 at 90iterations 4.6955771E-03 0.1650276 at 100iterations 2.3626345E-03 9.2895508E-02 at 110iterations 1.2748154E-03 5.1399231E-02 at 120iterations finished qdiffx linear iterations at : 08:23:18 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.2748154E-03 5.1399231E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 08:23:19 9.350u 0.252s 0:10.25 93.6% 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 Tue Oct 11 2011 at 08:23:19 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 268 has a net charge of -0.0940 !!! WARNING: GLM 272 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.832190 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 2.832190 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2463 net assigned charge : 4.812012 assigned positive charge : 393.3969 centred at (gu) : 89.19068 85.30157 90.35304 assigned negative charge : -388.5853 centred at (gu) : 89.65598 84.81911 91.00025 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22075 grid for indexing accessible points = 1.400000 m= 88852 mr = 129234 m= 31381 mr = 73399 m= 7272 mr = 25394 m= 904 mr = 5407 m= 43 mr = 558 m= 0 mr = 22 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 5616 time to turn everything in is 1.470000 number of dielectric boundary points 69930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19703 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) : 1.888127 object centre at (A) : 24.33400 32.08400 29.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3154939 0.1266988 midg,1,midg; midg,igrid,midg 0.2278343 0.2627248 1,midg,midg; igrid,midg,midg -7.7924393E-02 -0.1753557 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.840000 now iterating at: 08:23:21 rms-change max change #iterations 9.828710 340.1667 at 10iterations 5.662684 115.8921 at 20iterations 3.252268 65.85838 at 30iterations 1.865038 41.21766 at 40iterations 1.068942 22.93515 at 50iterations 0.6131380 13.50450 at 60iterations 0.3503981 6.478314 at 70iterations 0.2002858 3.569431 at 80iterations 0.1147587 2.139938 at 90iterations 6.5915361E-02 1.231249 at 100iterations 3.7650567E-02 0.6941681 at 110iterations 2.1639135E-02 0.4562645 at 120iterations 1.2505709E-02 0.2202358 at 130iterations 7.2794263E-03 0.1489944 at 140iterations 4.3109641E-03 8.7036133E-02 at 150iterations 2.6160255E-03 5.7510376E-02 at 160iterations 1.6561704E-03 3.7666321E-02 at 170iterations 1.1156501E-03 2.9991150E-02 at 180iterations finished qdiffx linear iterations at : 08:23:35 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 1.1156501E-03 2.9991150E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 08:23:35 15.771u 0.321s 0:16.44 97.8% 0+0k 0+0io 0pf+0w