> 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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>> > 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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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Mar 18 2011 - 15:00:03 PDT
