Karolyn's
My colleague Mihaly Mezei implemented a 2D rmsd comparison of two trajectories.
Please contact him. Mihaly.mezei.mssm.edu
I used it and it's a great tool
Roman Osman
Sent from my iPhone
> On Feb 11, 2016, at 4:45 AM, Karolina Markowska <markowska.kar.gmail.com> wrote:
>
> Thank you, Bill and Anselm for your advices,
>
> I think I will try the 2D-RMSD-plot first.
>
> Have a nice day!
> Karolina
>
> 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
>
>> Dear Karolina,
>>
>> AFAIK a 'reference' is limited to a single structure.
>>
>> Reading in two trajectories in a row should be no problem for cpptraj,
>> as you can give several trajin commands.
>> For the comparison of the two trajectories you could then use e.g. a
>> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> with a subsequent inspection of the distribution of the cluster
>> structures between the trajectories. Or you could monitor some other
>> properties of interest and compare those values.
>>
>> Regards,
>>
>> Anselm
>>
>>
>> Am 11.02.2016 10:07, schrieb Karolina Markowska:
>>> Dear Amber Users,
>>>
>>> I have two simulations with the same system and I would like to compare
>>> them. Mostly I would like to check if I'm having the same protein
>>> conformations in these two simulations. Does Amber software provide a
>> tool
>>> for that kind of analysis?
>>>
>>> I wanted to use cpptraj and use the first trajectory as reference, add
>> the
>>> second one by trajin and calculate rmsd between them, but cpptraj uses
>> only
>>> the first frame from that file. Can I make cpptraj to read whole
>> trajectory
>>> as a reference?
>>> The script looked like that:
>>>
>>> parm protein.prmtop
>>> reference sim1.nc
>>> trajin sim2.nc
>>> autoimage
>>> strip :WAT
>>> strip :Na+
>>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>>> quit
>>>
>>> | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>>> trajectory from the second simulation.
>>>
>>> Thanks for your help.
>>> Best regards,
>>> Karolina Markowska
>>> PhD student
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Received on Thu Feb 11 2016 - 08:00:05 PST
