remarks Set up thioredoxin


topology  
  @TOPPAR:amber/topamber.inp 
  @TOPPAR:amber/patches.pro
end

parameter @TOPPAR:amber/paramber.gb.inp end

segment
        name="    "
        chain
        link ppgp head - GLY tail + PRO end
        link ppgg head - GLY tail + GLY end
        link pepp head - * tail + PRO end
        link ppg2 head - GLY tail + * end
        link ppg1 head - * tail + GLY end
        link pept head - * tail + * end
        coordinates @trx.pdb
        end
end

patch nser refe=nil=(resid 1) end
patch nter refe="+"=(resid 1) end
patch ntr2 refe="-"=(resid 1) refe="+"=(resid 2) end

patch cala refe=nil=(resid 108) end
patch cter refe="-"=(resid 108) end

patch disu refe="1"=(resid 32) refe="2"=(resid 35) end

coordinates  @trx.pdb

write psf output=trx.psf end


stop

parameter
nbonds 
atom cdie trunc eps=1. 
e14fac=0.8333333   ! use this to reproduce elec term to amber
cutnb=9999. ctonnb=9996. ctofnb=9997.
nbxmod=3 vswitch
end
end

hbuild select=(resid 26 and name hd2) end


parameter nbonds EPS=1. WEPS=78.5 
         offset=0.09
         gbhct 
end end



flags include ace end



energy end


minimize powell nstep=50 end


write coor output=trxM.pdb end


stop

