Dear Lachele,
Thank you so much for your patience. I will come back to this question 1
hour latter, I have something urgent.
Best regards,
Rui
On Wed, Aug 21, 2019 at 1:40 PM Lachele Foley <lf.list.gmail.com> wrote:
> 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 - 13:00:05 PDT
