Hi Javi,

The latest parameters are attached. The prep file contains a 6YS.


On Mon, Oct 22, 2018 at 10:43 AM Javier Lopez <[log in to unmask]>

> Dear Mr./Mrs.
> We are trying to build “heparin sulfate octasaccharide” using its GLYCAM
> website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and
> xleap; but by the moment, this is impossible.
> Exactly, we are using the next sequence:
> DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH
> The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM builder as
> ‘6YS’), which is not detected in xleap and the following message appears
> (The YS residue is unknown):
> Warning: Unknown residue: 6YS number: 2 type: terminal/beginning
> ... relaxing end constraints to try for a dbase match
> ...
> ...
> Warning: -no luck
> ...
> ...
> Warning: one sided connection. Residue (default_name) missing connect1
> atom.
> Can you help us?
> If you need anything else, please let me know.
> Kind regards and have a good day.
> Javi