I presume you mean "what is the purpose of buliding oligosaccharides
using GLYCAM-Web?". If you want to know why you need to source a
GLYCAM parameter set, I can answer that too, but it's a different and
longer answer.
If you are willing to learn tleap, you don't need the website in most
cases, but the more complex oligosaccharides can become painful to
build using tleap, and casual modelers probably don't want to bother
with tleap at all. In short, the purpose of the site is to simplify
modeling for people, whether they are seasoned modelers or brand new
(and intimidated even by a monosaccharide).
But...
There aren't always PDB files for sugars at all. And, when there are,
the files often represent only one of several (or many) conformers
present in solution. That is, GLYCAM-Web provides a structures that
are difficult to obtain experimentally. It can also help you to
ensure that a monosaccharide in a PDB file is the one it claims to be
by comparing structures.
Even with a monosaccharide hexose the exocyclic torsions can occupy 2
or 3 rotamers. Of course, as you might have noticed, the website
currently doesn't provide multiple rotamers for monosaccharides, but
it could. No one has yet asked for that. Anyhow...
Did you ever use this command?
saveamberparm MAN MAN.parm7 MAN.rst7
That command is the real test, as it provides the files necessary for
MD simulations. In amber14, I notice that it renames the ROH residue,
but still builds as if it is the two residues (this is good). It
doesn't add ROH hydrogen well, no matter how I try loading your pdb
file, but a quick minimization will fix that. I didn't try any
earlier versions of tleap.
On Mon, May 25, 2015 at 9:52 AM, Chris <dlutlife223.163.com> wrote:
> Dear All!
>
> Simply put:
> If I have a a-D-mannose Monosaccharide in my pdb file goes that:
>
> HETATM 4532 C1 MAN A1277 44.674 66.009 49.225 0.50 18.65 C
> HETATM 4533 C2 MAN A1277 44.414 66.755 47.946 0.50 11.67 C
> HETATM 4534 C3 MAN A1277 42.968 66.536 47.566 0.50 9.58 C
> HETATM 4535 C4 MAN A1277 42.596 65.084 47.553 0.50 11.02 C
> HETATM 4536 C5 MAN A1277 42.882 64.500 48.925 0.50 17.80 C
> HETATM 4538 O1 MAN A1277 44.065 66.677 50.300 0.50 21.39 O
> HETATM 4537 C6 MAN A1277 42.247 63.221 49.363 0.80 16.97 C
> HETATM 4539 O2 MAN A1277 45.230 66.211 46.968 0.50 14.32 O
> HETATM 4540 O3 MAN A1277 42.647 67.158 46.339 0.50 8.06 O
> HETATM 4541 O4 MAN A1277 41.199 64.988 47.295 0.50 9.50 O
> HETATM 4542 O5 MAN A1277 44.275 64.669 49.215 0.50 19.81 O
> HETATM 4543 O6 MAN A1277 43.058 62.461 48.518 0.80 14.19 O
>
> I can successfully load this file with tleap after several steps:
> 1): just change residue name from 'MAN' to '0MA' except atom O1
> 2): change residue name from 'MAN' to 'ROH' for atom O1
> 3): mv atom O1 to the top
>
> then this file looks like:
>
> HETATM 4538 O1 ROH A1277 44.065 66.677 50.300 0.50 21.39 O
> HETATM 4532 C1 0MA A1277 44.674 66.009 49.225 0.50 18.65 C
> HETATM 4533 C2 0MA A1277 44.414 66.755 47.946 0.50 11.67 C
> HETATM 4534 C3 0MA A1277 42.968 66.536 47.566 0.50 9.58 C
> HETATM 4535 C4 0MA A1277 42.596 65.084 47.553 0.50 11.02 C
> HETATM 4536 C5 0MA A1277 42.882 64.500 48.925 0.50 17.80 C
> HETATM 4537 C6 0MA A1277 42.247 63.221 49.363 0.80 16.97 C
> HETATM 4539 O2 0MA A1277 45.230 66.211 46.968 0.50 14.32 O
> HETATM 4540 O3 0MA A1277 42.647 67.158 46.339 0.50 8.06 O
> HETATM 4541 O4 0MA A1277 41.199 64.988 47.295 0.50 9.50 O
> HETATM 4542 O5 0MA A1277 44.275 64.669 49.215 0.50 19.81 O
> HETATM 4543 O6 0MA A1277 43.058 62.461 48.518 0.80 14.19 O
>
> Then:
> 4): source leaprc.GLYCAM_06j-1
> 5): MAN=loadpdb man.pdb
>
> All thing goes well with such steps, and tleap successfully generate the parameter file for my pdb.
> #################################################################################################
> What I am confused is about the manual:
>
> manual said when we make paramers for sugar, we should do something like that:
>
> 1): source leaprc.GLYCAM_06j-1
> 2) MAN = sequence {ROH 0MA}
> 3)saveoff MAN man.lib or savepdb MAN man.pdb
>
> But I don't know how to go next: how can I make tleap recognize my sugar residue in pdb file with method written in manual ??
> I can simply change the residue names for sugars to make tleap recognize them, so what is the purpose of buliding oligosaccharides using GLYCAM? (If the sugars is not complex)
>
> Thx!
> Appreciate for your reply!
> Chris
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon May 25 2015 - 18:30:02 PDT
