remarks changed Tue Sep 2 09:48:07 CDT 2003 remarks by jfd to include a fes residue !@generate_tmoc.inp topology reset end structure reset end topology {===>} @TOPPAR:topallhdg5.3.pro end ! no chain id. segment name=" " chain @TOPPAR:topallhdg5.3.pep sequence @1xxx.seq end end chain sequence ZIN end end end ! removes the hydrogen on the cys-en ! and changes the atom type from SH1E to S. !patch DISN reference=1=( resid 18 ) ! reference=2=( resid 21 ) ! end ! turn doubly protonated his to singly protonated histidine (HD1) !patch HISD reference=nil=( resid 34 ) ! reference=nil=( resid 40 ) ! end patch ZINC reference=1=( resid 18 ) reference=2=( resid 21 ) reference=3=( resid 34 ) reference=4=( resid 40 ) reference=5=( resid 68 ) end ! turn peptide from trans to cis !patch CISP reference=nil=( resid 80 ) end evaluate ( $par_nonbonded = "OPLSX" ) parameter reset end parameter @TOPPAR:parallhdg5.3.pro end !coor @1xxx_xplor.pdb ! show everything is consistent (or not) !energy end ! print thres=0.05 bonds ! print thres=5. angles ! print thres=5. impropers ! print thres=140 dihe !coor init sele ( all ) end write psf output=1xxx.psf end stop ! junk not reached by script. print thres=0.05 bonds print thres=5. angles print thres=0.5 impropers print thres=140 dihe