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On Mon, Oct 22, 2018 at 4:53 AM Oliver Grant <[log in to unmask]> wrote:

> Hi Javi,
>
> The latest parameters are attached. The prep file contains a 6YS.
>
> Best,
> Oliver
>
>
> On Mon, Oct 22, 2018 at 10:43 AM Javier Lopez <[log in to unmask]>
> wrote:
>
>> 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
>>
>

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA