Hi all,
>
> I am trying to get an average structure from an md trajectory. I had
> seen the email seen below from Tom and I was trying to follow these
> instructions. However the structure that I'm getting for the average
> isn't right, it looks as if it hasn't been fit to the initial structure
> correctly. My understanding was that the command:
>
> rms first mass out allatoms_rmstofirst.dat *
>
> should change the coordinates of the structures in the trajectory so that they are fit to the first frame, but this doesn't seem to be the case. Do I need to trajin allatoms_rmstofirst.dat
> before finding the average?
>
> Thanks in advance.
>
> -- Holly Freedman
>
>
>
> Thomas E. Cheatham, III wrote:
>
>>>> >>>... to get the RMSd
>>>> >>>to the average structure is has to be done in two runs, the first to
>>>> >>>generate the average structure
>>>> >>>
>>>> >>> trajin annealing.traj 175 200
>>>> >>> average average.pdb pdb
>>>> >>>
>>>> >>>
>>>
>>>
>>> >>Does 'average' automatically rms fit each frame to the 1st?
>>> >>
>>> >>Normally one would want to fit to the 1st frame before adding
>>> >>coordinates to avoid drift and rotation artifacts. Once an
>>> >>average structure is obtained, it is worth visualizing it
>>> >>to check for artifacts of internal motions, and then energy
>>> >>minimizing it in order to get reasonable bond lengths etc.
>>> >>
>>> >>
>>
>>
>> >
>> >Yes, Bill is right here. Before doing the average you definately want to
>> >fit otherwise the average structure could be meaningless.
>> >
>> > trajin annealing.traj 175 200
>> > rms first mass out allatoms_rmstofirst.dat *
>> > average average.pdb pdb *
>> >
>> >Thanks for pointing this out Bill!
>> >
>> >--tom
>
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Received on Tue May 18 2004 - 22:53:00 PDT
