Hi,
I've done a test with VMD 1.8.7 and PTRAJ from AT 1.4.
run0.pdb from run0.rst7 (last frame of run0.nc).
PTRAJ:
trajin run0.nc
reference run0.pdb
rms reference out rmsd.dat .N,CA,C time 1.0
VMD:
Trajectories:
0 run0.pdb
1 run0.nc
RMSD Trajectory Tool:
Ref: Selected (highlighted run0.pdb in trajectory list)
Trajectory Frame ref: 0
Selection: all (also checked backbone)
The deviation between the RMSD values generated by VMD and those
generated by PTRAJ is < 0.001. Are you absolutely certain you have the
correct reference selected in VMD?
-Dan
On Wed, Oct 6, 2010 at 1:22 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi Dan,
> here I am proving you the detail which you were asking:
>
> 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?
> I used the RMSD Trajectory tool. In that I first aligned the trajectories to
> the pdb generated using ambpdb after equilibration. Then I calculated the
> rmsd for the backbone atoms (Backbone atom definition: C CA N) And I got the
> rmsd in the range of 6-8.
>
> 2) For ptraj, send your complete ptraj.in.
>
> trajin prod1.crd
> reference eq2.pdb
> rms reference out rmsd_to_lowest_energy_struct.dat .N,CA,C time 1.0
>
>
> Hirdesh
>
>>
>>
>>
>>
>
>
>>
>> -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 Wed Oct 06 2010 - 16:00:06 PDT
