Thanks for your help ,you can call me Guang.I come from China.
------------------ ???????? ------------------
??????: "lloyd riggs"<lloyd.ri...@gmx.ch>;
????????: 2012??8??31??(??????) ????7:25
??????: "Discussion list for GROMACS users"<gmx-users@gromacs.org>;
????: Re: [gmx-users] Glycoproteion MD
Dear (sorry cant read chinese),
You can find some OPLS or 53a6 Parameters on the web by doing extensive
searches, mostly they are free, but hosted on varied individual lab web sites.
That, or it may be easier to define some sets of bonds (angles, dihedrials,
lengths charges, etc...from either the CRC or national institute of standards)
for a small subset of sugars, inclusive of the inter-chain bonds, and then just
use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for
phosphorylated to sugar, etc... as inclusive this would only be several to a
dozen atom types or somthing)....(then you can post it :-))...but it might be
easier than trying to define things based on single sugar moieties available on
the web, as you most likely would have errors when your suger moities are large
from the inter-sugar bonds between subunits, such as a 10-20 length
polysacharide on a glycosylated protein. This is less trivial than it might
seem, but would still take a few days, and you might be able to
use all but say 1-2 atoms if you find several defined parameters for sugars on
the web already...
Sincerely,
Stephan Watkins
-------- Original-Nachricht --------
> Datum: Fri, 31 Aug 2012 09:26:38 +0800
> Von: "??????" <525342...@qq.com>
> An: "gmx-users" <gmx-users@gromacs.org>
> Betreff: [gmx-users] Glycoproteion MD
> Dear all I am interested in simulating a model of Glycoproteion. I
> could'nt find the define of the residue in any forcefield .rtp file of GMX. I
> am
> using Gromacs 4.5.5 . If any one can help me in getting forcefield
> parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please
> suggest where else I should search for these.
>
> Thanking all
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