Dear Raj,
You could use the building block approach and R.E.D. Server Dev./PyRED
at
http://q4md-forcefieldtools.org/REDServer-Development/
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
A phosphate group contains a negative total charge: I would vote for
splitting each monosaccharide and the phosphate into two different
building blocks involved in charge derivation...
regards, Francois
> we want to use the GLYCAM forcefield for phosphorylated carbohydrates. The
> lastest AMBER manual mentions in the table on page 36 that phospate
> parameters exist in the GLYCAM force field, and it seems that there is
> published work "out there" that uses such parameters. However, we could
> not apply the phospate derivate button on the GLYCAM carbohydrate builder,
> whereas the sulfate, acetyl or methyl groups seem to work flawlessly. Can
> we somehow use the builder or do we need to derive our own parameters? Can
> somebody give us a tip on how to get started?
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Received on Wed Jun 18 2014 - 00:00:02 PDT
