Dear Lachelle and Francois,
thanks for the quick replies.
.Lachelle
I think our main point of confusion is/was the lack of a "PO3" residue
in the GLYCAM force field files, while there is one for "SO3". We have
used the AMBER protein force field as well as GAFF in the past, however,
obviously the usual simple AMBER workflow that we are used to (have a
PDB file with correct AMBER residue names and let leap assign atom types
based on residue templates) does not work in our case here. So it seems
that we need to assign atom types manually and individually for each
atom using leap's "set" command, like you did in that example.
.Francois
"I would vote for splitting each monosaccharide and the phosphate into
two different building blocks involved in charge derivation..."
I think this is what we will do. In this case the PO4 moiety should be
simply reusable with other sugars if we want to play around with these
later on. However, as far as I understand things, we will need to
construct several different carbohydrate-phosphates and perform the ESP
fit process simultaneously for all of them, subject to the constraints that
-the partial charges of all atoms of the carbohydrate moiety retain
their original GLYCAM-defined value,
-the partial charges of all atoms of the phosphate moiety are the same
for each carbohydrate-phosphate and
-the sum of the partial charges of the phosphate moiety is equal to the
integer total charge of the carbohydrate-phosphate minus the sum of the
partial charges of the carbohydrate moiety. That would mean using inter-
as well as intramolecular charge constraints in "RED-parlance" and the
process should be similar to J. Org. Chem. 2007, 72, 9032-9045 by Gouin
et al and your tutorial "V.4- Force field for a set of glycoconjugate
fragments", right?
Best regards,
Raj Schneider & Jochen Heil,
TU Dortmund,
Germany
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Received on Wed Jun 18 2014 - 02:30:02 PDT
