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Re: [cnsbb] peptide bond cut during annealing

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  • Nic
    Yes. I have had this happen when I had to create a novel amino acid (oxidized cysteine) and didn t set it up to link with the normal amino acids.
    Message 1 of 4 , Mar 5, 2012
      Yes. I have had this happen when I had to create a novel amino acid
      (oxidized cysteine) and didn't set it up to 'link' with the normal amino
      acids.

      On 3/4/2012 8:15 PM, Ed Pozharski wrote:
      > Most likely, there is some error in topology. Please post your
      > topology/parameter/link files for the unconventional residue.
      >
      > On Sun, 2012-03-04 at 20:18 +0000, feher_krisztina wrote:
      >>
      >> Dear All,
      >>
      >> I was generated topologies/parameters for a new residue in a peptide.
      >> The generate.inp created a correct peptide bond from the new residue
      >> to the next residue in the generated .pdb file and produced an .mtf
      >> file, which I used as an input for the anneal.inp. During the
      >> annealing the peptide bond was not hold in place anymore and the
      >> peptide was severed into two pieces. Anyone has any idea where the
      >> problem could be?
      >>
      >> Thanks a lot for any help,
      >> Krisztina
      >>
      >>
      >>
      >>
      >>
      >
      >
      >
      > ------------------------------------
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    • Krisztina Feher
      Hi Nic, thanks a lot! This was the solution as you suggested: I forgot to add the new residue into the link file to be patched with PEPT. SInce the involved
      Message 2 of 4 , Mar 5, 2012
        Hi Nic,

        thanks a lot! This was the solution as you suggested: I forgot to add the new residue into the link file to be patched with PEPT. SInce the involved atoms were still close in the .pdb file after generate.inp, it was shown as a bond being there, but the .mtf did not list those bonds/angles/etc..

        Thanks again,
        Krisztina

        --- On Mon, 3/5/12, Nic <csteussy@...> wrote:

        From: Nic <csteussy@...>
        Subject: Re: [cnsbb] peptide bond cut during annealing
        To: cnsbb@yahoogroups.com
        Cc: "feher_krisztina" <feher_krisztina@...>
        Date: Monday, March 5, 2012, 11:11 AM

         

        Yes. I have had this happen when I had to create a novel amino acid
        (oxidized cysteine) and didn't set it up to 'link' with the normal amino
        acids.

        On 3/4/2012 8:15 PM, Ed Pozharski wrote:
        > Most likely, there is some error in topology. Please post your
        > topology/parameter/link files for the unconventional residue.
        >
        > On Sun, 2012-03-04 at 20:18 +0000, feher_krisztina wrote:
        >>
        >> Dear All,
        >>
        >> I was generated topologies/parameters for a new residue in a peptide.
        >> The generate.inp created a correct peptide bond from the new residue
        >> to the next residue in the generated .pdb file and produced an .mtf
        >> file, which I used as an input for the anneal.inp. During the
        >> annealing the peptide bond was not hold in place anymore and the
        >> peptide was severed into two pieces. Anyone has any idea where the
        >> problem could be?
        >>
        >> Thanks a lot for any help,
        >> Krisztina
        >>
        >>
        >>
        >>
        >>
        >
        >
        >
        > ------------------------------------
        >
        > --------------------------------------------------------
        > List information at http://groups.yahoo.com/group/cnsbb.
        > Posting is only allowed for members of this list.
        >
        > Yahoo! Groups Links
        >
        >
        >

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