that make me clear. thank you for your help!
On Fri, Mar 18, 2011 at 4:42 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> The following link describes the current GLYCAM naming convention.
>
> http://glycam.ccrc.uga.edu/ccrc/pages/cncg.html
>
>
> On Fri, Mar 18, 2011 at 5:40 PM, Lachele Foley (Lists)
> <lf.list.gmail.com> wrote:
> >> But the PDB file says 4GA 2; OLA 3
> >> It seems 4GA (galactose) is assigned as residue 2 and OLA (glucose) is 3
> >
> >
> > The residue called 4GA is a 4-linked alpha glucose.
> >
> > The residue called 0LA (that's zero-L-A), is a non-reducing end
> > terminal alpha galactose.
> >
> >
> > On Fri, Mar 18, 2011 at 5:24 PM, Bingwu Yu <amber.qna.gmail.com> wrote:
> >> Thanks! I used glycam to buildup the molecue.
> >> But the PDB file says 4GA 2; OLA 3
> >> It seems 4GA (galactose) is assigned as residue 2 and OLA (glucose) is 3
> >> anyway I will modify the ptraj_in file try again.
> >>
> >> On Fri, Mar 18, 2011 at 5:08 PM, Lachele Foley (Lists) <
> lf.list.gmail.com>wrote:
> >>
> >>> If you're using standard Glycam residues, the C1 and Ox will be in
> >>> different residues. So, the first one looks better.
> >>>
> >>> However, you might have your residue numbers confused. In Glycam, the
> >>> residue sequence is backwards from what people usually write. The
> >>> molecule beta-galactose-1-4-alpha-glucose would be:
> >>>
> >>> m = sequence { ROH 4GA 0LB }
> >>>
> >>> So, atoms O4 and C4 would be in residue 2, with H1 and C1 being in
> residue
> >>> 3.
> >>>
> >>> If you aren't using Glycam, then that might or might not be the issue.
> >>>
> >>>
> >>> On Fri, Mar 18, 2011 at 4:30 PM, Bingwu Yu <amber.qna.gmail.com>
> wrote:
> >>> > so I am able to load output crd with VMD and check dihedral angles
> for 4
> >>> > atoms. But comparing the value calculated from VMD for the same frame
> >>> does
> >>> > not match the value extracted by ptraj.
> >>> > the molecule I use is alpha-lactose, which is
> >>> > beta-galactose-1-4-alpha-glucose
> >>> > The four atoms to define phi are H1, C1 from galactose and O4 C4 from
> >>> > glucose
> >>> >
> >>> > the ptraj_in file is
> >>> >
> >>> > *trajin md_output.crd 25 125 1
> >>> > dihedral phi :2.H1 :2.C1 :3.O4 :3.C4 out aLac_phi.out
> >>> > go*
> >>> >
> >>> > Is this file correct? I got another version from tutorial is
> >>> >
> >>> > *trajin md_output.crd 25 125 1
> >>> > dihedral phi :2.H1 :3.C1 :3.O4 :3.C4 out aLac_phi.out
> >>> > go*
> >>> > _______________________________________________
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> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> :-) Lachele
> >>> Lachele Foley
> >>> CCRC/UGA
> >>> Athens, GA USA
> >>>
> >>> _______________________________________________
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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Mar 18 2011 - 21:30:04 PDT
