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[ccp4bb]: A summary of the "non-proline peptide bond" question



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dear all,
this is a summary of the replies to the "non-proline peptide bond":

1. Many people suggested me to use REFMAC5 becasue it can do it
   automatically.
2. Some people gave me the toppar parameters to handle the situation,
   and some people even kindly provided their toppar files to me.

---------------------------
1) Boaz Shaanan wrote:
 Try this:

 parameter

  dihedral (name ca and resid 88) (name c and resid 88)
 (name n and resid 89) (name ca and resid 89)  1250. 2 180.
  end

 This defines a cis-peptide between residues 88 and 89. It worked for me both
in Xplor and CNS.
----------------------------
2) Manfred Weiss wrote:

For refinement in CNS you have to have an extra parameter file
which looks something like :

 parameter
     angl (name CA and resid $res1) (name C  and resid $res1)
          (name N  and resid $res2)
     485.856     119.700

     angl (name C  and resid $res1) (name N  and resid $res2)
          (name CA and resid $res2)
      599.823    127.800

     angl (name O  and resid $res1) (name C  and resid $res1)
          (name N  and resid $res2)
     759.150     120.600


     dihe (name CA and resid $res1) (name C  and resid $res1)
          (name N  and resid $res2) (name CA and resid $res2)
     1250.0      2    180.0
 end
------------------------------
------------------------------
3) R Natesh wrote:
   Create a new file cis_peptide.param (see below) and  read
this parameter file in refinement ".inp" file after
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param" !(... etc.  as)
{===>} parameter_infile_2="cis_peptide.param";

cis_peptide.param file below
---------
! param
        dihedral ( name ca and resid 10 )  ( name c and resid 10 )
                 ( name n and resid 11 ) ( name ca and resid 11 )
                 1250. 2 180.
! end
---------

-------------------------------
4) Gomis-Rueth F.Xavier wrote:
just write

parameter
  dihedral (name CA and resid 360) (name C and resid 360)
  (name N and resid 361) (name CA and resid 361)
  5. 2 180
end

after having read in your parameters and you will get a cis-peptide
bond between residues 360 and 361.
--------------------------------
5) Rene M. de Jong wrote:

When you want to put a cis-peptide (non-proline) in the refinement in
cns,
proceed as follows:

In refine.inp:

put the dihedral definition in the script between the following lines in

refine.inp:

____________________________________________________

   structure @&structure_infile end
   coordinates @&coordinate_infile

 end if

<<<< put statement here!


 xray

   @CNS_XTALLIB:spacegroup.lib (sg=&sg;
                                sgparam=$sgparam;)


____________________________________________________


Put the following dihedral definition in there (this is
an example for two molecules in the ASU, with a cis-pep
between residue 183 and 184:

____________________________________________________

 {* any special protein patches can be applied here *}
{===>}

parameter
 dihedral ( name ca and segid "A" and resid 183 )
         ( name  c and segid "A" and resid 183 )
         ( name  n and segid "A" and resid 184 )
         ( name ca and segid "A" and resid 184 )
           1250.0 1 180.0
end

parameter
 dihedral ( name ca and segid "B" and resid 183 )
         ( name  c and segid "B" and resid 183 )
         ( name  n and segid "B" and resid 184 )
         ( name ca and segid "B" and resid 184 )
           1250.0 1 180.0
end

{<===}

____________________________________________________

6) Samantha Greasley wrote:
You need a parameter file similar to the one you can
get out of the script cis_peptide.inp. It looks like
this:

{===========================================================}

set echo=off message=off end

{===========================================================}
{===========================================================}
!>>>> cis-peptide: segid="A" resid=432 resname=ASN
!>>>>              current dihedral value=    0.400

!to maintain this geometry use the
!  following parameter statement during refinement:

dihedral ( name ca and segid "A" and resid 431 )
         ( name  c and segid "A" and resid 431 )
         ( name  n and segid "A" and resid 432 )
         ( name ca and segid "A" and resid 432 )
           1250.0 1 180.0

{===========================================================}

set echo=on message=on end


All you have to do is include this parameter file in the refinement
input files,eg:

{* parameter files *}
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
{===>} parameter_infile_2="CNS_TOPPAR:water_rep.param";
{===>} parameter_infile_3="CNS_TOPPAR:ion.param";
{===>} parameter_infile_4="cis_peptide.param";

--------------------------------------------------------------

7) Takaaki Fukami wrote:
If you're using TOPPAR/protein.top and TOPPAR/protein_rep.param files,
the easist way I think is to modify the protein_rep.param as below.
(add last 4 lines)  You don't need define a special residue for cis-pept.

{ very tight/rigid dihedrals }
dihe X    C    NH1  X     $kdih_rigid   1     0.0 ! omega torsion angle and
ARG...
dihe CH1E C    N    CH1E  $kdih_rigid   2   180.0 ! allow cis PRO
dihe CH2E C    N    CH1E  $kdih_rigid   2   180.0
dihe CH2G C    N    CH1E  $kdih_rigid   2   180.0

dihe CH1E C    NH1  CH1E  $kdih_rigid   2   180.0 ! allow cis Pept
dihe CH2G C    NH1  CH1E  $kdih_rigid   2   180.0 !
dihe CH1E C    NH1  CH2G  $kdih_rigid   2   180.0 ! cis GLY
dihe CH2G C    NH1  CH2G  $kdih_rigid   2   180.0 !

8) Bernie wrote: (and attatched a cis_peptide.inp file)

You need to run cis_peptide.inp to assign it in the structure.

Also, refine.inp doesn't read the file, so I only use minimize.inp and
individual-bref.inp for refinement.  anneal.inp also works with a cis-peptide.


I've attached my cis_peptide.inp file.  It creates a cis_peptide.param that
you reference with the other parameter files.


Thanks all the people kindly replied my questions.

Rong-Jin Guan