Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER

From: Lachele Foley (Lists) <"Lachele>
Date: Thu, 13 Jan 2011 09:36:35 -0500

Ptraj should be able to do most of this. I'm not sure about the dcd
file format. Check the list of options for "trajout." I believe you
mean a dcd format associated with CHARMM. Ptraj will output a charmm
binary trajectory. I think VMD will read/write dcd formats if ptraj
won't, but I can't promise that.

I recommend opening the AmberTools manual and searching on terms like
"gyration" and "cluster". These will lead you, in fairly short order,
to the proper ptraj commands. You might also scan the list of
commands to see which will be useful for you. For example, you can
strip the protein out using a residue mask in much the same way as you
stripped the waters. The "center" command will center on the glycan
if you use the appropriate mask. It might take a little creativity,
but you should be able to do it.

Persons with more ptraj experience than me might have additional comments.

:-) Lachele

On Thu, Jan 13, 2011 at 12:27 AM, Anindya Sarkar <> wrote:
> Hi Everybody,
> I am running the MD simulations of a glycosylated protein using AMBER force
> field ff99SB and GLYCAM_06. Can anybody tell me how to analyze the different
> properties of the glycosidic residues of the glycosylation like RMSD, Radius
> of gyration, dihedral angle calculation, cluster analysis, glycomaps etc
> using AMBER or any other software package?
> I have run my simulations with the NetCDF format of the trajectory and I
> have already used ptraj for stripping the water and ions but anybody can
> tell me how to extract the glycosylation only trajectory devoid of the
> protein molecule and how can I put the glycans at the center of the
> trajectory like the proteins with the command "image center familiar" in
> ptraj. Whether this glycosylation only trajectory can be saved as dcd
> extension file also.
> Thanks in advance.
> Anindya
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Jan 13 2011 - 07:00:05 PST
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