[X-plor] cis bond

bb232 at msstate.edu bb232 at msstate.edu
Tue Apr 11 22:45:52 EST 2006


Hi all,

I am calculating a protein structure from NMR data using anneal.inp with CNS.
>From NOE data, there is a cis peptide bond between G101 and G102.
>From the crystal struture the CA, C, N, CA dihedral angle should be 0.0°. From
the CNS calculation I am getting a trans peptide bond.
I have tried the following to force cis peptide bond.

1. in gereate_seq.inp file the following patch was added.

      patch cisp
      reference + (residue 101) reference - (residue 102)
      end

This patch seems to have been impemented, however we get trans.

2. I have tried a parameter file (cis-peptide.param) as follows:

      dihe ( name CA and resid 101) (name C and resid 101) (name N and resid
102)( name CA and resid 102) 1250.0 1 0
      end
This seemed to be read in however, ignored during the calculation and I still
get trans.

3. I have also tryed different combinations of 1 and 2 with no sucess.

4. I have been able to force CNS to form this cis dihedral angle by adding the
following to the dehedral restraint file.

       assign (resid 101 and name CA) (resid 101 and C) (resid 102 and name N)
       (resid 102 and name CA) 10 0.00 5 2

       which resulted in a cis peptide with a huge improper violations due to
distortion of the NH and CO bonds.

Does anyone have any suggestion on how to fix my problem?

Thank you for you help,

Bulent Binbuga

Mississippi State Universty

bb232 at msstate.edu






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