Do you still need help with this?
On Fri, Jul 5, 2019 at 11:25 AM Rui Chen <rchen6.ualberta.ca> wrote:
>
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Aug 21 2019 - 13:00:04 PDT
