* loneprtest.inp * Author: Bernard R. Brooks * Files : None * Tests : Lone pair facility * bomlev -2 stream datadir.def read rtf card * TOPOLOGY FILE FOR lone pair test * 18 1 ! Classification from AB MASS 1 H 1.00800 ! hydrogen which can h-bond to neutral atom MASS 2 HC 1.00800 ! - " - charged atom RESI CEN1 0.00000 GROU ATOM H1 H 0.1 RESI CEN2 0.00000 GROU ATOM H1 H 0.0 ATOM H2 H 0.1 RESI CEN3 0.00000 GROU ATOM H1 H 0.0 ATOM H2 H 0.0 ATOM H3 H 0.1 RESI CEN4 0.00000 GROU ATOM H1 H 0.0 ATOM H2 H 0.0 ATOM H3 H 0.0 ATOM H4 H 0.1 END read parameter card * parameter file for lonepair test * BOND H H 0.0 1.0 THETAS H H H 0.0 90.0 PHI H H H H 0.0 2 180.0 IMPHI H H H H 0.0 0 0.0 NONBONDED NBXMOD 5 ATOM CDIEL SWITCH VATOM VDISTANCE VSHIFT - CUTNB 20.0 CTOFNB 17.5 CTONNB 13.5 EPS 1.0 E14FAC 1.0 WMIN 1.5 ! H 0.0440 0.0 0.8000 END read sequence card * two 2-center sets * 2 CEN4 CEN4 generate a setup read coor card * coordinate for first test * 8 1 1 CEN4 H1 0.00000 0.00000 0.00000 A 1 0.00000 2 1 CEN4 H2 0.00000 1.00000 0.00000 A 1 0.00000 3 1 CEN4 H3 0.00000 1.00000 1.00000 A 1 0.00000 4 1 CEN4 H4 1.00000 1.00000 1.00000 A 1 0.00000 5 2 CEN4 H1 3.00000 3.00000 3.00000 A 2 0.00000 6 2 CEN4 H2 3.00000 3.00000 2.00000 A 2 0.00000 7 2 CEN4 H3 2.00000 3.00000 2.00000 A 2 0.00000 8 2 CEN4 H4 2.00000 2.00000 2.00000 A 2 0.00000 coor copy comp energy test first step 0.00001 tol 0.0 !!!!!!!! test fixed option !!!!!!!! coor copy lonepair fixed A 1 H4 lonepair fixed A 2 H4 lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test center option !!!!!!!! coor copy lonepair center A 1 H4 sele resid 1 .and. .not. type H4 end lonepair center A 2 H4 sele resid 2 .and. .not. type H4 end lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test colocate option !!!!!!!! coor copy lonepair colocate sele type h4 end sele type h3 end lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test colinear dist option !!!!!!!! coor copy lonepair colinear DIST 0.5 - sele type h4 end sele type h3 end sele type h2 end lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test colinear scale option !!!!!!!! coor copy lonepair colinear scale -0.5 - sele type h4 end sele type h3 end sele type h2 end lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test cen2 option !!!!!!!! coor copy lonepair cen2 sele type h4 end sele type h3 end sele type h2 end lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test relative option !!!!!!!! coor copy lonepair relative sele type h4 end sele type h3 end - sele type h2 end sele type h1 end - DIST 1.0 ANGLE 90.0 DIHE 90.0 lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test bisector option !!!!!!!! coor copy lonepair bisector sele type h4 end sele type h3 end - sele type h2 end sele type h1 end - DIST 1.0 ANGLE 60.0 DIHE 100.0 lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor lonepair clear !!!!!!!! test relative option with random coords !!!!!!!! random gaussian 0.7 iseed 258261 scalar x random scalar y random scalar z random coor add lonepair relative sele type h4 end sele type h3 end - sele type h2 end sele type h1 end - DIST 1.25 ANGLE 75.0 DIHE 98.0 lonepair print coor shake energy test first step 0.00001 tol 0.0 print coor !!!!!!!! tests lonepair I/O !!!!!!!! print psf open write card unit 20 name @9loneprtest.psfc1 write psf card unit 20 ! test deletion of a lonepair delete atom sele atom a 1 h4 end print psf ! test binary write open write file unit 21 name @9loneprtest.psfb1 write psf file unit 21 open write card unit 22 name @9loneprtest.psfc3 write psf card unit 22 ! test read psf append rename segid B sele segid a end open read card unit 20 name @9loneprtest.psfc1 read psf card unit 20 append print psf ! test deletion of a lonepair host (error message desired) delete atom sele atom B 2 H1 end print psf ! test reading then writing open read card unit 20 name @9loneprtest.psfc1 read psf card unit 20 open write card unit 20 name @9loneprtest.psfc2 write psf card unit 20 ! test binary read delete atom sele all end open read file unit 21 name @9loneprtest.psfb1 read psf file unit 21 open write card unit 22 name @9loneprtest.psfc4 write psf card unit 22 ! Note: ! c1 and c2 should be the same ! c3 and c4 should be the same !!!!!!!! end of tests !!!!!!!! stop