Dear List,
I obtained parameters and charges for a sulphated tetrasaccharide
(ROH-PGA-PGA-PGA-PGA) with sulphates at O2, O3 and O4 position using GLYCAM
website. The glycosidic linkages is alpha 1->4.
Instead of ROH, we want to attach a lipophilic linker group -O-CH2-CH2-CH3.
I understand that glycam terminal groups (ROH) connected to the sugar have
a total charge of -0.194.
I am trying to derive RESP charges for the lipophilic group using PyRED
script. I have capped the group as CH3-O-CH2-CH2-CH3. In the
project.config script I am using following constraints where atoms 1 to 3
are for CH3 and atom 4 represents oxygen. The charge on glycosidic oxygen
of lipophilic chain is now restrained to -0.4680, same as the charge on the
of O4 atom of PGA residue.
MOLECULE1-INTRA-MCC2 = 0.0 | 1 2 3 4 | Remove
MOLECULE1-INTRA-MCC2 = -0.4680 | 5 | keep
I am adding -0.194 to -0.4680 after getting optimised output from PyRed
script. Therefore the charge on oxygen of linker group is -0.6620.
Can anyone comment if this is a valid approach to derive charges of the
linker (lipophilic segment)? Note that the charges for PGA tetrasaccharide
are taken from glycam webserver.
Many thanks,
Neha S. Gandhi
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Received on Sun Apr 08 2018 - 23:30:02 PDT
