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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>>> 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 - 15:00:04 PDT
