Dear David,
I downloaded the original pdb file from PDB data bank, without any
modification (say, adding glycans, adding ions, solvate the system). I
double checked the distance between these four CYS. The distance between
resid 128:SG and 182:SG is 2.036 *Å*, the distance between resid 16:SG and
82:SG is 2.029 *Å. *It seems like my modification changed the position of
these CYS. Does it really matter? Maybe I also changed the position of the
other residues.
Best regards,
Rui
On Fri, Jul 5, 2019 at 9:01 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Jul 04, 2019, Rui Chen wrote:
> >
> >As you can see in the output file, I got warnings about improper torsions.
> >How to solve the problem? Thank you.
>
> You can ignore these messages. But note you got some additional
> warnings about the diulfide bonds:
>
> Checking Unit.
> WARNING: There is a bond of 3.361144 angstroms between:
> ------- .R<CYX 16>.A<SG 8> and .R<CYX 82>.A<SG 8>
> WARNING: There is a bond of 3.502353 angstroms between:
> ------- .R<CYX 128>.A<SG 8> and .R<CYX 182>.A<SG 8>
>
> These problems will probably go away upon minimization, but, if they are
> unexpected, you might want to investigate. Do you expect your structure
> to have well-formed disulfide bonds with about a 2 Ang. bond length?
>
> ....dac
>
>
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Received on Fri Jul 05 2019 - 08:30:03 PDT
