Sun Oct 9 06:52:10 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 06:52:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6720405 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): -24.74000 26.47700 ymin,ymax (A): 1.688000 46.39700 zmin,zma (A): -23.65600 29.31700 x,y,z range (A): 51.21700 44.70900 52.97300 scale (grids/A): 0.6720405 object centre (A): 0.8685007 24.04250 2.830500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 89.23329 89.28183 88.75272 assigned negative charge : -302.1561 centred at (gu) : 89.16899 89.50785 88.70057 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6099 nv = 96 ne = 84 npr = 42078 no. pairs analyzed = 42078 no. exposed pairs = 2470 no. arc points = 17721 no. surface atoms = 843 nbur = 1158 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3371 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.2600000 number of dielectric boundary points 3039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1665 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7026 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5434359E-08 1.4588136E-09 midg,1,midg; midg,igrid,midg 4.3280295E-08 -4.9081965E-08 1,midg,midg; igrid,midg,midg -2.6037705E-08 3.7811678E-09 gauss-seidel spectral radius is 0.9884675 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 06:52:11 rms-change max change #iterations 0.1636792 30.72287 at 10iterations 1.7899537E-02 2.704498 at 20iterations 1.9877648E-03 0.3051567 at 30iterations 2.1743127E-04 3.5671234E-02 at 40iterations 2.3865136E-05 3.7612915E-03 at 50iterations finished qdiffx linear iterations at : 06:52:14 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.3865136E-05 3.7612915E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:52:14 3.407u 0.200s 0:04.07 88.4% 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 Sun Oct 9 2011 at 06:52:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.016121 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): -24.74000 26.47700 ymin,ymax (A): 1.688000 46.39700 zmin,zma (A): -23.65600 29.31700 x,y,z range (A): 51.21700 44.70900 52.97300 scale (grids/A): 2.016121 object centre (A): 0.8685007 24.04250 2.830500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 87.69989 87.84572 86.25793 assigned negative charge : -302.1561 centred at (gu) : 87.50683 88.52375 86.10178 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17721 grid for indexing accessible points = 1.400000 m= 23679 mr = 44960 m= 3922 mr = 17516 m= 244 mr = 2538 m= 6 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1697 time to turn everything in is 0.4900000 number of dielectric boundary points 28124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14757 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) : 0.6720405 object centre at (A) : 0.8685007 24.04250 2.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3056590E-02 2.6807230E-02 midg,1,midg; midg,igrid,midg 4.7719594E-02 -3.8500231E-02 1,midg,midg; igrid,midg,midg -4.8420157E-02 -3.1562443E-03 gauss-seidel spectral radius is 0.9987166 estimated iterations to convergence 221 setup time was (sec) 0.7900000 now iterating at: 06:52:15 rms-change max change #iterations 4.167672 175.4076 at 10iterations 1.988850 86.30957 at 20iterations 0.9511930 31.95901 at 30iterations 0.4557958 16.46923 at 40iterations 0.2183940 7.136210 at 50iterations 0.1048805 3.487764 at 60iterations 5.0162360E-02 1.889980 at 70iterations 2.3945022E-02 0.8858442 at 80iterations 1.1486527E-02 0.3791685 at 90iterations 5.4876171E-03 0.1803377 at 100iterations 2.6354003E-03 8.5438728E-02 at 110iterations 1.2567361E-03 4.5992851E-02 at 120iterations finished qdiffx linear iterations at : 06:52:22 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.2567361E-03 4.5992851E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 06:52:23 7.724u 0.242s 0:08.40 94.7% 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 06:52:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.024182 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): -24.74000 26.47700 ymin,ymax (A): 1.688000 46.39700 zmin,zma (A): -23.65600 29.31700 x,y,z range (A): 51.21700 44.70900 52.97300 scale (grids/A): 3.024182 object centre (A): 0.8685007 24.04250 2.830500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 86.55003 86.76849 84.38689 assigned negative charge : -302.1561 centred at (gu) : 86.26025 87.78561 84.15270 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 150965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17721 grid for indexing accessible points = 1.400000 m= 75974 mr = 108472 m= 27951 mr = 62418 m= 7354 mr = 22672 m= 1097 mr = 5583 m= 76 mr = 718 m= 0 mr = 36 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 5261 time to turn everything in is 1.220000 number of dielectric boundary points 63518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 14896 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) : 2.016121 object centre at (A) : 0.8685007 24.04250 2.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5762069 0.4253615 midg,1,midg; midg,igrid,midg 0.5694564 -0.4315529 1,midg,midg; igrid,midg,midg -0.4406846 6.9136404E-02 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.530000 now iterating at: 06:52:24 rms-change max change #iterations 9.462037 407.5144 at 10iterations 5.446053 117.9195 at 20iterations 3.138703 63.49419 at 30iterations 1.807087 39.79517 at 40iterations 1.041387 18.30168 at 50iterations 0.5985237 10.74064 at 60iterations 0.3455468 6.664167 at 70iterations 0.1985100 3.715101 at 80iterations 0.1142400 2.179880 at 90iterations 6.5732226E-02 1.299067 at 100iterations 3.7759330E-02 0.7596169 at 110iterations 2.1808833E-02 0.4039822 at 120iterations 1.2525000E-02 0.2356319 at 130iterations 7.2048269E-03 0.1401405 at 140iterations 4.1510481E-03 8.1268311E-02 at 150iterations 2.3888226E-03 5.1999092E-02 at 160iterations 1.3773845E-03 2.5917053E-02 at 170iterations 7.9438969E-04 1.5707016E-02 at 180iterations finished qdiffx linear iterations at : 06:52:35 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 7.9438969E-04 1.5707016E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 06:52:36 12.404u 0.242s 0:12.96 97.5% 0+0k 0+0io 0pf+0w