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

From: Anindya Sarkar <>
Date: Thu, 13 Jan 2011 10:29:43 -0500

Hi Lachele,

Thanks for your mail. Do you have any scirtpt file that you have told me to
stip the protein out and for the centering of the glycosylation command. And
for this purpose I am assuming that a prmtop with only glycosylation should
be needed for the analyses. Can you give me any idea how to generate the
glycosylation only prmtop from the prmtop file of the glycosylated protein.

Thanks again.

On Thu, Jan 13, 2011 at 9:36 AM, Lachele Foley (Lists) <>wrote:

> 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
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Received on Thu Jan 13 2011 - 08:00:03 PST
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