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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Received on Thu Aug 26 2010 - 10:30:06 PDT
