Dear Neha,
See
http://q4md-forcefieldtools.org/REDServer-Development/faq.php#5
When describing the problem you encountered with R.E.D. Server
Development, please also provide the 'PXXXX' R.E.D. Server Development
job name in the body of your email so that we can more easily assist
you.
> 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.
So if I understand you you want to replace that ROH group... RO group;
right? which has a -0.194 total charge.
> 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.
You want to generate a O-CH2-CH2-CH3 fragment from the
"CH3"-O-CH2-CH2-CH3 molecule; so remove that "CH3" group.
You want a total charge = -0.194 for O-CH2-CH2-CH3;
-> that means +0.194 for the "CH3" group to be removed.
"CH3"-O-CH2-CH2-CH3
".194"-0.194 = 0 for the whole molecule
MOLECULE1-INTRA-MCC1 = 0.194 | 1 2 3 4 | Remove
1 2 3 4 are the supposed indexes of the "CH3" group.
-> no need to equivalence 1 2 3 4 (because atoms are simply
removed and not used in MD) -> MCC1
(I would use INTRA-MCC1 because the RRMS should be slightly better)
http://q4md-forcefieldtools.org/REDServer-Development/popup/popkeyword.php
I would select "CHR_TYP=RESP-C2" in the System.config file.
and _carefully_ compare the RRMS of the fit without intra-mcc vs that
with intra-mcc.
I hope I understood your problem: Indeed I want to underline that at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#29 the O1 atom
belongs to the sugar unit and _not_ to the aglycon part
(
https://en.wikipedia.org/wiki/Aglycone)...
regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Tue Apr 10 2018 - 06:00:02 PDT
