In order to really assess what is going on here more information is required.
1) In VMD, which module did you use to calculate RMSD (RMSD Tool or
RMSD Trajectory Tool), what selection did you use, what options did
you have checked, and what structure was chosen as your reference?
2) For ptraj, send your complete ptraj.in.
-Dan
On Tue, Oct 5, 2010 at 2:25 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi Kshatresh,
> Sorry for incomplete Information. In my previous mail I forgot to mention
> that the I am getting high value in VMD and the low value is from Ptraj of
> amber. I did not calculated the average structure of the entire run, I just
> calculated the pdb structure after the equilibration phase. Do I need to
> calculate the average structure of the entire run and then calculate the
> rmsd w.r.t. to that structure.
>
>
> Hirdesh
>
> On Tue, Oct 5, 2010 at 11:29 AM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com>wrote:
>
>> Hi Hirdesh,
>>
>> May i know at which simulation time have u saved your pdb? Have u
>> calculated
>> average structure of complete simulation?
>>
>> On Tue, Oct 5, 2010 at 11:21 AM, hirdesh kumar <hirdeshs8.gmail.com>
>> wrote:
>>
>> > Hi All,
>> > I calculated the rmsd for my protein of interest by aligning it to the
>> pdb
>> > generated after equilibration. The value of rmsd is very high when i
>> > calculated for backbone atoms (i.e. Calpha, N) in the range of 6-8. The
>> > same
>> > calculation using amber ptraj module gave me the rmsd value of around one
>> > throughout the production phase.
>> > Now I am wondering which one should I take for my further consideration.
>> >
>> >
>> > Hirdesh
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>> >
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Received on Tue Oct 05 2010 - 07:30:02 PDT
