Tue Oct 11 04:55:09 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 Tue Oct 11 2011 at 04:55:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6402763 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): 17.06200 72.66300 ymin,ymax (A): 41.47900 87.52299 zmin,zma (A): 4.351000 59.85400 x,y,z range (A): 55.60100 46.04399 55.50300 scale (grids/A): 0.6402763 object centre (A): 44.86250 64.50100 32.10250 number of atom coordinates read : 2646 total number of charged atoms : 2523 net assigned charge : 13.00003 assigned positive charge : 403.6689 centred at (gu) : 90.41929 89.93324 91.41379 assigned negative charge : -390.6696 centred at (gu) : 90.41409 89.61450 91.38335 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7210 nv = 96 ne = 84 npr = 52798 no. pairs analyzed = 52798 no. exposed pairs = 3297 no. arc points = 22901 no. surface atoms = 1110 nbur = 1536 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 4012 m= 0 mr = 43 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3300000 number of dielectric boundary points 3574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2305 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1624548E-08 3.0490259E-08 midg,1,midg; midg,igrid,midg -2.0211646E-08 5.4645007E-08 1,midg,midg; igrid,midg,midg 1.6934926E-08 2.1475161E-08 gauss-seidel spectral radius is 0.9873642 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 04:55:10 rms-change max change #iterations 0.1468411 20.47529 at 10iterations 1.4653308E-02 1.999063 at 20iterations 1.4608909E-03 0.2160358 at 30iterations 1.4736420E-04 2.3036957E-02 at 40iterations 1.6441691E-05 2.3994446E-03 at 50iterations finished qdiffx linear iterations at : 04:55:13 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.6441691E-05 2.3994446E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 04:55:14 3.731u 0.205s 0:04.48 87.7% 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 Tue Oct 11 2011 at 04:55:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.920829 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): 17.06200 72.66300 ymin,ymax (A): 41.47900 87.52299 zmin,zma (A): 4.351000 59.85400 x,y,z range (A): 55.60100 46.04399 55.50300 scale (grids/A): 1.920829 object centre (A): 44.86250 64.50100 32.10250 number of atom coordinates read : 2646 total number of charged atoms : 2523 net assigned charge : 13.00003 assigned positive charge : 403.6689 centred at (gu) : 91.25758 89.79948 94.24095 assigned negative charge : -390.6696 centred at (gu) : 91.24223 88.84309 94.15003 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22901 grid for indexing accessible points = 1.400000 m= 28644 mr = 54326 m= 4700 mr = 21158 m= 242 mr = 2905 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 303 time to turn everything in is 0.6000000 number of dielectric boundary points 33055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19866 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) : 0.6402763 object centre at (A) : 44.86250 64.50100 32.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3081800E-02 5.2649494E-02 midg,1,midg; midg,igrid,midg -1.6890543E-02 7.3577568E-02 1,midg,midg; igrid,midg,midg 1.2210411E-02 -2.1417341E-03 gauss-seidel spectral radius is 0.9986639 estimated iterations to convergence 217 setup time was (sec) 0.9300000 now iterating at: 04:55:15 rms-change max change #iterations 4.307597 205.3471 at 10iterations 2.045527 66.93520 at 20iterations 0.9673109 31.15326 at 30iterations 0.4572877 16.59977 at 40iterations 0.2159781 6.485345 at 50iterations 0.1023229 3.315422 at 60iterations 4.8409343E-02 1.636666 at 70iterations 2.2952568E-02 0.7193074 at 80iterations 1.0865053E-02 0.3121109 at 90iterations 5.1288367E-03 0.1695423 at 100iterations 2.4230448E-03 7.6822281E-02 at 110iterations 1.1515139E-03 3.3779144E-02 at 120iterations finished qdiffx linear iterations at : 04:55:22 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 1.1515139E-03 3.3779144E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 04:55:23 8.321u 0.255s 0:09.07 94.4% 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 04:55:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.881243 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): 17.06200 72.66300 ymin,ymax (A): 41.47900 87.52299 zmin,zma (A): 4.351000 59.85400 x,y,z range (A): 55.60100 46.04399 55.50300 scale (grids/A): 2.881243 object centre (A): 44.86250 64.50100 32.10250 number of atom coordinates read : 2646 total number of charged atoms : 2523 net assigned charge : 13.00003 assigned positive charge : 403.6689 centred at (gu) : 91.88604 89.69895 96.36130 assigned negative charge : -390.6696 centred at (gu) : 91.86332 88.26460 96.22501 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 179887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22901 grid for indexing accessible points = 1.400000 m= 92392 mr = 131300 m= 34085 mr = 75817 m= 8335 mr = 27353 m= 1070 mr = 6165 m= 51 mr = 687 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1158 time to turn everything in is 1.540000 number of dielectric boundary points 74491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 20177 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) : 1.920829 object centre at (A) : 44.86250 64.50100 32.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1286783 0.3553025 midg,1,midg; midg,igrid,midg -0.2199588 0.6201500 1,midg,midg; igrid,midg,midg 7.1313061E-02 -2.2326799E-02 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.890000 now iterating at: 04:55:25 rms-change max change #iterations 10.08695 392.2921 at 10iterations 5.901041 134.9843 at 20iterations 3.426061 75.26337 at 30iterations 1.995713 38.26219 at 40iterations 1.157957 26.88401 at 50iterations 0.6707668 13.46352 at 60iterations 0.3873518 6.883095 at 70iterations 0.2240131 4.314617 at 80iterations 0.1296412 2.593679 at 90iterations 7.4783608E-02 1.397762 at 100iterations 4.3078482E-02 0.7740488 at 110iterations 2.4867596E-02 0.4371033 at 120iterations 1.4358565E-02 0.3428545 at 130iterations 8.2746875E-03 0.1542835 at 140iterations 4.7678379E-03 8.8169098E-02 at 150iterations 2.7605228E-03 5.1389694E-02 at 160iterations 1.5958598E-03 3.0822754E-02 at 170iterations 9.2578644E-04 1.6815186E-02 at 180iterations finished qdiffx linear iterations at : 04:55:37 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 9.2578644E-04 1.6815186E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 04:55:38 13.844u 0.253s 0:14.50 97.1% 0+0k 0+0io 0pf+0w