On Tue, Mar 20, 2012 at 2:30 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> In building a topology file, I get the following disulfide bond warnings:
>
> Checking Unit.
> WARNING: There is a bond of 3.493686 angstroms between:
> ------- .R<CYX 19>.A<SG 8> and .R<CYX 54>.A<SG 8>
> WARNING: There is a bond of 3.201259 angstroms between:
> ------- .R<CYX 50>.A<SG 8> and .R<CYX 108>.A<SG 8>
> WARNING: There is a bond of 3.240445 angstroms between:
> ------- .R<CYX 97>.A<SG 8> and .R<CYX 117>.A<SG 8>
> WARNING: The unperturbed charge of the unit: -8.998000 is not zero.
>
> Is it safe to disregards them?
>
Are any of them unexpected to you? (Visualizing is typically very helpful
with this)
If they are not unexpected, these are fine.
HTH,
Jason
>
> Note that the original pdb file was built by means of homology modelling.
>
> Many thanks for any suggestions
>
> George
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 20 2012 - 16:30:03 PDT
