Mon Oct 10 16:58:41 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 Mon Oct 10 2011 at 16:58:41 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 0.6751887 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 0.6751887 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2196 net assigned charge : -2.568997 assigned positive charge : 336.5653 centred at (gu) : 89.37502 88.88374 89.89821 assigned negative charge : -339.1349 centred at (gu) : 89.42973 88.80316 89.93887 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 = 45962 no. pairs analyzed = 45962 no. exposed pairs = 3027 no. arc points = 21030 no. surface atoms = 1018 nbur = 1260 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 3887 m= 8 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2700000 number of dielectric boundary points 3684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6483913E-10 -1.9497314E-08 midg,1,midg; midg,igrid,midg -3.7891940E-08 8.3113756E-09 1,midg,midg; igrid,midg,midg 4.8139368E-09 -2.0693651E-08 gauss-seidel spectral radius is 0.9886043 estimated iterations to convergence 76 setup time was (sec) 0.6100000 now iterating at: 16:58:42 rms-change max change #iterations 0.1713575 27.87088 at 10iterations 1.9477418E-02 3.112618 at 20iterations 2.0885200E-03 0.3139706 at 30iterations 2.4773093E-04 3.8673401E-02 at 40iterations 3.4404642E-05 4.2724609E-03 at 50iterations finished qdiffx linear iterations at : 16:58:46 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 3.4404642E-05 4.2724609E-03 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 16:58:48 5.247u 0.438s 0:06.98 81.2% 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 Mon Oct 10 2011 at 16:58:48 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 2.025566 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 2.025566 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2196 net assigned charge : -2.568997 assigned positive charge : 336.5653 centred at (gu) : 88.12454 86.65112 89.69444 assigned negative charge : -339.1349 centred at (gu) : 88.28908 86.40953 89.81661 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21030 grid for indexing accessible points = 1.400000 m= 29071 mr = 52233 m= 5608 mr = 21289 m= 492 mr = 3603 m= 13 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1118 time to turn everything in is 0.6400000 number of dielectric boundary points 33862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17399 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) : 0.6751887 object centre at (A) : 23.31500 21.56450 18.62600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0768352E-03 -3.1923484E-02 midg,1,midg; midg,igrid,midg -4.4104304E-02 1.3915533E-02 1,midg,midg; igrid,midg,midg 6.3674748E-02 8.3890976E-03 gauss-seidel spectral radius is 0.9987645 estimated iterations to convergence 225 setup time was (sec) 0.9900000 now iterating at: 16:58:54 rms-change max change #iterations 4.446136 208.3009 at 10iterations 2.156464 65.50452 at 20iterations 1.054921 34.42203 at 30iterations 0.5111778 16.60608 at 40iterations 0.2488109 8.143559 at 50iterations 0.1212591 3.981644 at 60iterations 5.8743116E-02 1.769827 at 70iterations 2.8710637E-02 0.9154177 at 80iterations 1.4052403E-02 0.4178772 at 90iterations 6.8137329E-03 0.1909983 at 100iterations 3.3133230E-03 9.8869324E-02 at 110iterations 1.6191886E-03 5.4052353E-02 at 120iterations finished qdiffx linear iterations at : 16:59:07 total time elapsed so far: 13.14000 # loops : 120 mean,max change (kT/e) : 1.6191886E-03 5.4052353E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 16:59:07 13.312u 0.516s 0:19.21 71.9% 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 Mon Oct 10 2011 at 16:59:07 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2278 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 3.038349 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): -3.048000 49.67800 ymin,ymax (A): -1.818000 44.94700 zmin,zma (A): -4.413000 41.66500 x,y,z range (A): 52.72600 46.76500 46.07800 scale (grids/A): 3.038349 object centre (A): 23.31500 21.56450 18.62600 number of atom coordinates read : 2278 total number of charged atoms : 2196 net assigned charge : -2.568997 assigned positive charge : 336.5653 centred at (gu) : 87.18669 84.97663 89.54149 assigned negative charge : -339.1349 centred at (gu) : 87.43365 84.61423 89.72491 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 175501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21030 grid for indexing accessible points = 1.400000 m= 90303 mr = 126575 m= 36517 mr = 73431 m= 10528 mr = 29324 m= 2038 mr = 7952 m= 212 mr = 1365 m= 13 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 3794 time to turn everything in is 1.750000 number of dielectric boundary points 76340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 17564 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) : 2.025566 object centre at (A) : 23.31500 21.56450 18.62600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0072962E-03 -0.2750865 midg,1,midg; midg,igrid,midg -0.3350554 0.2877484 1,midg,midg; igrid,midg,midg 0.7305464 0.1581661 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 16:59:10 rms-change max change #iterations 10.21687 411.3257 at 10iterations 6.035828 126.5983 at 20iterations 3.575138 75.99785 at 30iterations 2.096997 37.00468 at 40iterations 1.237623 28.22393 at 50iterations 0.7258613 13.79028 at 60iterations 0.4261752 8.409277 at 70iterations 0.2497014 4.368629 at 80iterations 0.1457702 2.504417 at 90iterations 8.5106649E-02 1.632217 at 100iterations 4.9902782E-02 0.8792958 at 110iterations 2.9057950E-02 0.5224228 at 120iterations 1.7004726E-02 0.3066902 at 130iterations 9.9017406E-03 0.1775570 at 140iterations 5.7875891E-03 0.1013060 at 150iterations 3.3839922E-03 5.6400299E-02 at 160iterations 1.9825392E-03 3.3476353E-02 at 170iterations 1.1684393E-03 2.0904541E-02 at 180iterations finished qdiffx linear iterations at : 16:59:29 total time elapsed so far: 21.13000 # loops : 180 mean,max change (kT/e) : 1.1684393E-03 2.0904541E-02 energy calculations done at 21.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.30000 DelPhi exited at 16:59:30 21.308u 0.544s 0:22.43 97.3% 0+0k 0+0io 0pf+0w