[AMBER] chirality restraints for non-standard residue

From: Jio M <jiomm.yahoo.com>
Date: Fri, 16 Apr 2010 04:15:08 -0700 (PDT)

Dear users,

I have joined    chiral residue with a peptide bond to
another residue. As I did annealing the configuration changed at the
chiral center as expected. So I want to apply chiral restraints to the
chiral center and want peptide bond to be trans

I have seen by command make_CHIRAL_RST for normal protein pdb.

&rst iat=23,22,3,2,

   r1=150., r2=170., r3=190., r4=210., rk2 = 50., rk3=50.,  &end


I am not able to get meaning of r1 r2 etc. If I am not wrong iat
represents atom number and also they represent CA-N(of first amino
acid)-C-CA (of second amino acid) that is CA-N--C-CA the peptide bond.
Can I similarly do for my residues. What about r1, r2 r3 here???

PLease suggest

regards JIomm

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Received on Fri Apr 16 2010 - 04:30:02 PDT
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