Hello all,
I am trying to calculate the relative binding energy of methyl-fucose w.r.t
fucose using TI integration.
Coordinate file for alpha-L-fucose sugar accoring to GLYCAM naming
convnetintion are like fallowing
ATOM 1 1HO ROH 1 2.144 0.950 -0.364 1.00 0.00
ATOM 2 O1 ROH 1 1.184 0.950 -0.364 1.00 0.00
ATOM 3 C1 0fA 2 1.154 -0.437 -0.084 1.00 0.00
ATOM 4 H1 0fA 2 2.168 -0.866 -0.126 1.00 0.00
ATOM 5 O5 0fA 2 0.313 -1.155 -0.937 1.00 0.00
*
* other atoms of 0fA in between this
*
ATOM 22 O2 0fA 2 1.493 0.186 2.300 1.00 0.00
ATOM 23 H2O 0fA 2 1.256 1.112 2.255 1.00 0.00
TER
Where as coordinate file for alpha-L-methy-fucose sugar accoring to GLYCAM
naming convnetintion are like fallowing
ATOM 1 H1 OME 1 1.789 2.304 -1.671 1.00 0.00
ATOM 2 CH3 OME 1 1.746 1.224 -1.578 1.00 0.00
ATOM 3 H2 OME 1 2.735 0.782 -1.633 1.00 0.00
ATOM 4 H3 OME 1 1.148 0.782 -2.368 1.00 0.00
ATOM 5 O OME 1 1.184 0.950 -0.364 1.00 0.00
ATOM 6 C1 0fA 2 1.154 -0.437 -0.084 1.00 0.00
ATOM 7 H1 0fA 2 2.168 -0.866 -0.126 1.00 0.00
*
* other atoms of 0fA in between this
*
ATOM 25 O2 0fA 2 1.493 0.186 2.300 1.00 0.00
ATOM 26 H2O 0fA 2 1.256 1.112 2.255 1.00 0.00
I am planning to transform atom :ROH.1HO (from fucose) into OME.CH3,H1,H2,H3
(in methyl fucose) during the step two of the thermodynamic integration.
During the transformation oxygen of fucose which have hydrohen atom
:ROH.1HO(in fucose) will be replaced by --CH3 group :OME.CH3,H1,H2,H3
(in methyl fucose). I am afraid about the oxygen atom (atom 2 in pdb) in
fucose ":ROH.O1" because, i am not including this oxygen in transformation
(removing charge from it, transformation and again adding charges) , but
the same oxygen (atom 5 in pdb file) is named as as ":OME.O" in
methyl-fucose. My doubt is in the atom and residue name of the oxygen
(where --H will be replaced CH3) becuse its also changing from fucose
(ROH.O1) to methyl-fucose ":OME.O". So should i also include this atome
during the transformation and I shold go for transformation --OH to --OCH3 ?
or this change is not going to effcet my results ?
Thankinh You
Sushil
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Received on Fri Jan 15 2010 - 09:30:04 PST
