Sun Oct 9 02:44:06 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 Sun Oct 9 2011 at 02:44:06 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2167 !!! WARNING: SEP 162 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.0940 !!! WARNING: HIT 185 has a net charge of 0.5140 !!! WARNING: MG5 517 has a net charge of 1.4000 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: 0.6362710 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): -16.79400 23.57700 ymin,ymax (A): 1.168000 44.31500 zmin,zma (A): -19.51200 36.43900 x,y,z range (A): 40.37100 43.14700 55.95100 scale (grids/A): 0.6362710 object centre (A): 3.391500 22.74150 8.463502 number of atom coordinates read : 2167 total number of charged atoms : 2029 net assigned charge : -3.154987 assigned positive charge : 326.6886 centred at (gu) : 90.42601 90.41829 90.71127 assigned negative charge : -329.8439 centred at (gu) : 90.40183 90.41162 90.69140 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5808 nv = 96 ne = 84 npr = 45441 no. pairs analyzed = 45441 no. exposed pairs = 2438 no. arc points = 16988 no. surface atoms = 838 nbur = 1329 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 3389 m= 0 mr = 35 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2600000 number of dielectric boundary points 2669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1659 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1070512E-09 -2.7377056E-09 midg,1,midg; midg,igrid,midg -4.3497637E-09 -3.8733563E-09 1,midg,midg; igrid,midg,midg -5.7750609E-09 -2.1643631E-09 gauss-seidel spectral radius is 0.9871593 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 02:44:07 rms-change max change #iterations 0.1327092 20.54917 at 10iterations 1.2866816E-02 1.898384 at 20iterations 1.2601225E-03 0.2114427 at 30iterations 1.2544295E-04 2.0827293E-02 at 40iterations 1.2329573E-05 1.7356873E-03 at 50iterations finished qdiffx linear iterations at : 02:44:11 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 1.2329573E-05 1.7356873E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 02:44:12 4.768u 0.373s 0:05.50 93.2% 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 Sun Oct 9 2011 at 02:44:12 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2167 !!! WARNING: SEP 162 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.0940 !!! WARNING: HIT 185 has a net charge of 0.5140 !!! WARNING: MG5 517 has a net charge of 1.4000 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: 1.908813 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): -16.79400 23.57700 ymin,ymax (A): 1.168000 44.31500 zmin,zma (A): -19.51200 36.43900 x,y,z range (A): 40.37100 43.14700 55.95100 scale (grids/A): 1.908813 object centre (A): 3.391500 22.74150 8.463502 number of atom coordinates read : 2167 total number of charged atoms : 2029 net assigned charge : -3.154987 assigned positive charge : 326.6886 centred at (gu) : 91.27765 91.25463 92.13366 assigned negative charge : -329.8439 centred at (gu) : 91.20553 91.23454 92.07419 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16988 grid for indexing accessible points = 1.400000 m= 22841 mr = 45398 m= 3595 mr = 17302 m= 180 mr = 2447 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1265 time to turn everything in is 0.5100000 number of dielectric boundary points 24639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 15975 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) : 0.6362710 object centre at (A) : 3.391500 22.74150 8.463502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0199362E-03 2.0615855E-02 midg,1,midg; midg,igrid,midg 2.8970017E-04 -8.0639906E-03 1,midg,midg; igrid,midg,midg -8.3204433E-03 -4.9864142E-03 gauss-seidel spectral radius is 0.9985865 estimated iterations to convergence 211 setup time was (sec) 0.7900000 now iterating at: 02:44:13 rms-change max change #iterations 3.928001 169.3797 at 10iterations 1.811766 72.49760 at 20iterations 0.8385808 32.15019 at 30iterations 0.3887606 13.83077 at 40iterations 0.1803470 5.655975 at 50iterations 8.3240181E-02 2.930532 at 60iterations 3.8516596E-02 1.297623 at 70iterations 1.7896686E-02 0.5871754 at 80iterations 8.2539665E-03 0.2900193 at 90iterations 3.8312320E-03 0.1295013 at 100iterations 1.7706382E-03 6.3158035E-02 at 110iterations 8.2447496E-04 2.8907776E-02 at 120iterations finished qdiffx linear iterations at : 02:44:23 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 8.2447496E-04 2.8907776E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 02:44:23 10.860u 0.442s 0:11.57 97.6% 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 Sun Oct 9 2011 at 02:44:23 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2167 !!! WARNING: SEP 162 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.0940 !!! WARNING: HIT 185 has a net charge of 0.5140 !!! WARNING: MG5 517 has a net charge of 1.4000 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: 2.863219 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): -16.79400 23.57700 ymin,ymax (A): 1.168000 44.31500 zmin,zma (A): -19.51200 36.43900 x,y,z range (A): 40.37100 43.14700 55.95100 scale (grids/A): 2.863219 object centre (A): 3.391500 22.74150 8.463502 number of atom coordinates read : 2167 total number of charged atoms : 2029 net assigned charge : -3.154987 assigned positive charge : 326.6886 centred at (gu) : 91.91649 91.88187 93.20053 assigned negative charge : -329.8439 centred at (gu) : 91.80836 91.85190 93.11128 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 146585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16988 grid for indexing accessible points = 1.400000 m= 74473 mr = 109658 m= 27038 mr = 62192 m= 6427 mr = 22235 m= 882 mr = 5075 m= 44 mr = 665 m= 0 mr = 14 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3991 time to turn everything in is 1.320000 number of dielectric boundary points 55610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 16231 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) : 1.908813 object centre at (A) : 3.391500 22.74150 8.463502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3706252 0.5165210 midg,1,midg; midg,igrid,midg 7.9006690E-04 -9.0463996E-02 1,midg,midg; igrid,midg,midg -0.1161451 -3.4368400E-02 gauss-seidel spectral radius is 0.9992267 estimated iterations to convergence 284 setup time was (sec) 1.650000 now iterating at: 02:44:25 rms-change max change #iterations 9.068146 339.6677 at 10iterations 5.155110 109.6007 at 20iterations 2.933152 69.94566 at 30iterations 1.667237 31.98943 at 40iterations 0.9454924 18.08788 at 50iterations 0.5365919 10.53057 at 60iterations 0.3040925 5.788562 at 70iterations 0.1722783 3.255730 at 80iterations 9.7653776E-02 2.021957 at 90iterations 5.5373043E-02 1.011578 at 100iterations 3.1490877E-02 0.5929813 at 110iterations 1.7847383E-02 0.3536377 at 120iterations 1.0132053E-02 0.1857181 at 130iterations 5.7422114E-03 0.1135669 at 140iterations 3.2547601E-03 6.4685822E-02 at 150iterations 1.8504520E-03 3.7113905E-02 at 160iterations 1.0506223E-03 2.2265911E-02 at 170iterations 5.9950160E-04 1.1686087E-02 at 180iterations finished qdiffx linear iterations at : 02:44:43 total time elapsed so far: 19.21000 # loops : 180 mean,max change (kT/e) : 5.9950160E-04 1.1686087E-02 energy calculations done at 19.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.37000 DelPhi exited at 02:44:43 19.376u 0.454s 0:20.13 98.4% 0+0k 0+0io 0pf+0w