Thanks Oliver
On Thu, Jan 13, 2011 at 11:37 AM, Oliver Grant <olivercgrant.gmail.com>wrote:
> *Do you have any scirtpt file that you have told me to
> stip the protein out and for the centering of the glycosylation command. *
>
> Use ptraj with your prmtop used to run the simulation. ptraj is simple
> enough and there is a tutorial that explains everything you need.
>
> *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.
> *
> To view the stripped .crd file you will need a matching prmtop. Alter your
> original leap.in file so that it saveamberparm's your glycan unit only (if
> that is what you are interested in). If you generated your structure on
> glycam.org they provide a leap.in file when you build your structure that
> you can modify and rerun tleap.
>
> Oliver
>
>
> On 13 January 2011 15:29, Anindya Sarkar <axs849.case.edu> wrote:
>
> > 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.
> > Anindya
> >
> > On Thu, Jan 13, 2011 at 9:36 AM, Lachele Foley (Lists) <
> lf.list.gmail.com
> > >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 <axs849.case.edu>
> > 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
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
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> > >
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> >
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Received on Thu Jan 13 2011 - 09:00:03 PST
