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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> > 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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Received on Fri Mar 18 2011 - 14:30:05 PDT
