Thank you for your clear answer, Jason!
Nadia
On Fri, Aug 1, 2014 at 3:15 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Aug 1, 2014 at 5:54 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
> > Hi Nadia,
> >
> > In AMBER FF the Cys group which has S-S linkage with another Cys
> > group has a residue name as CYX, which is different from CYS and CYM,
> > Another two Cys groups in AMBER FF. I guess the problem is about the
> > residue name in pdb file but not sure.
> >
> > Jason, can leap automatically assign the S-S bond to Cys residues which
> > has a CYS residue name in pdb file but has two S atoms are close to each
> > other?
> >
>
> The only bonds that tleap adds are:
>
> 1) Bonds defined in residue library files
> 2) Bonds defined by PDB CONECT records
> 3) Bonds you add with the "bond" command
>
> If you use "pdb4amber", that program may automatically add disulfide bonds
> here...
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 01 2014 - 15:30:03 PDT
