Dear Jochen,
> 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.
if you read:
http://q4md-forcefieldtools.org/REDDB/projects/F-87/
http://q4md-forcefieldtools.org/REDDB/projects/F-84/
http://q4md-forcefieldtools.org/REDDB/projects/F-72/
http://q4md-forcefieldtools.org/REDDB/projects/F-71/
not only "PO3" is 'missing': this is just a never ending problem ;-)
R.E.D. Server Dev./PyRED assigns force field atom types: either use
one of the different force field models, or provide your own
frcmod.user file in the archive file and your own force field atom
types in the Project.config file
(
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/Project.config MOLECULE1-ATMTYPE =
'...')
>> "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.
This is just the best choice and this was originally described by the
Kollman's group in Cieplak et al. (but not for sugars):
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
Sugar-OH Me-PO4(2-) -> Sugar + PO4(2-) -> Sugar-PO4(2-)
<--->
1 inter-mcc
Sugar-(OH)2 Me-PO4(2-) -> Sugar + PO4(2-) -> Sugar-[PO4(2-)]2
2 inter-mcc
etc...
> In this case the PO4 moiety should be
> simply reusable with other sugars if we want to play around with these
> later on.
Yes
> 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,
'retain GLYCAM-defined value'?
Just create your own force field - why do you need to retain what others did?
This is particularly true if you need to introduce different phosphate
groups in your oligosaccharide: retaining GLYCAM-defined value will
just introduce too many errors in the charge fitting step...
> -the partial charges of all atoms of the phosphate moiety are the same
> for each carbohydrate-phosphate and
the charge of the monosaccharide units are different and the charges
of the phosphate groups can be identical or different depending on the
number of building blocks used for the phosphate groups; that being
said - I would first simplify the problem and use a single building
block for the phosphate groups...
> -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?
Yes
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#29
http://q4md-forcefieldtools.org/Tutorial/PyRED/Glycocluster/Project.config
regards, Francois
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Received on Thu Jun 19 2014 - 02:00:02 PDT
