Re: [AMBER] Dihedral angles does not match VMD vs ptraj

From: Lachele Foley (Lists) <"Lachele>
Date: Fri, 18 Mar 2011 17:08:33 -0400

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 <> 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*
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Fri Mar 18 2011 - 14:30:03 PDT
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