dear Sir,
I try to solve my problame by that procedure,but it does not work . Whan
simulation is done the disaccharide molecule is dissociate.I do not found
any clue .I am trying to read more tutorials for this but???please help me
regarding this.
thanking you
subrata
On Thu, Aug 26, 2010 at 9:18 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Subrata,
>
> > I am totaly new in amber. I am going through the tutorials. I am
> able
> > to creat .prmtop and .inpcrd file for a disaccharide using glycam force
> > field in amber. Is it possible to creat .prmtop and .inpcrd for a
> > disaccharide using amber force field.
>
> I do not understand why you want to use 'the' Amber FF for studying
> carbohydrates as GLYCAM is devoted to this task. That being said, Yes,
> you can and there are examples of such an approach in the literature.
>
> > I can simulate one disaccharide with solvatebox in amber. I want
> to
> > simulate 10 disaccharide and 200 water , but i don't know how i increase
> > the number of disaccharide in the system and how i fixed the number of
> water
> > molecule?
>
> You could follow the approach below:
>
> xleap -f leaprc.GLYCAM_06
> TT1 = sequence { XXX XXX YYY } # XXX being the sugar unit you need
> savepdb TT1 TT1.pdb # YYY being the capping group
>
> The generated TT1.pdb PDB file with one disaccharide looks as it follows:
> Cartesian coordinates of
> XXX 1 residue 1
> XXX 2 residue 2
> YYY 3 residue 3
> TER
> END
>
> -------
>
> You copy TT1.pdb into TT2.pdb, you modify TT2.pdb as it follows
> XXX 1 residue 1
> XXX 2 residue 2
> YYY 3 residue 3
> TER
> XXX 4 residue 4
> XXX 5 residue 5
> YYY 6 residue 6
> END
> Then you add +1 (or any value) to all X Cartesian coordinates of
> residues 4, 5 & 6, keeping the Cartesian coordinates of residues 1, 2
> & 3 unchanged.
>
> => You can load the double disaccharide TT2.pdb in leap:
> xleap -f leaprc.GLYCAM_06
> TT2 = loadpdb TT2.pdb
> you can solvate, save prmtop/prmcrd files etc...
>
> -------
>
> same idea for three disaccharides:
> XXX 1 residue 1
> XXX 2 residue 2
> YYY 3 residue 3
> TER
> XXX 4 residue 4 +1 to X Cart. coordinates
> XXX 5 residue 5 +1 to X Cart. coordinates
> YYY 6 residue 6 +1 to X Cart. coordinates
> TER
> XXX 7 residue 7 +2 to X Cart. coordinates
> XXX 8 residue 8 +2 to X Cart. coordinates
> YYY 9 residue 9 +2 to X Cart. coordinates
> END
>
> etc...
>
> Then, instead of adding +1/+2 /+n to each X Cart. coordinates 2/3/n of
> disaccharide you might choose more sophisticated translation values.
>
> regards, Francois
>
>
>
>
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>
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Received on Thu Sep 02 2010 - 05:30:05 PDT
