AMBER Archive (2009)

Subject: Re: AMBER: RMS plot

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jan 06 2009 - 13:57:50 CST

fluctuations and rmsd values are not the same- fluctuations are
compared to the average structure during the time period, while rmsd
is compared to some arbitrary reference structure. often its true that
parts that are moving more give both higher flucs and higher rmsds,
but if one moves away from a reference and then stays there, you could
get low flucs and high rmsd.

On Tue, Jan 6, 2009 at 2:54 PM, Duggan, Brendan M. <bmduggan_at_musc.edu> wrote:
> I too have been trying to get per residue RMSDs from trajectories. After looking at the ptraj manual I was using commands like:
>
> trajin ./ligand.traj
> rms first :1-85
> atomicfluct out backbone.rmsd @N,CA,C byres
>
> This gave me numbers that seemed reasonable, but I'm not sure if its correct. Can anyone tell me the difference between these commands and what Carlos proposed?
>
> brendan
>
> email: bmduggan_at_musc.edu
> phone: (843) 792 5029
> fax: (843) 792 4322
>
> ________________________________________
> From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling [carlos.simmerling_at_gmail.com]
> Sent: Friday, January 02, 2009 9:08 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: RMS plot
>
> probably the easiest way is to make a script that creates a ptraj
> input for this, like the following. then you'll need to average the
> outputs, again a script will do that. maybe there is an easier way or
> someone else might have a better program- I don't think ptraj does it
> directly. hopefully you can use the example below as a starting place
> and modify it for your needs. make sure to watch out for the "nofit"
> parts and change the masks to what you want.
>
> #!/bin/csh
>
> set i=1
> set last = 100
> echo "ptraj prmtop << EOF"
> echo "trajin ./mdcrd.gz"
> echo "reference ./ref.crd"
>
> echo "rmsd reference mass out rmsd.res.ALL.dat :$i-$last"
> while ($i < 10)
> echo "rmsd reference mass out rmsd.res.all.00$i.dat :$i nofit"
> @ i++
> end
> while ($i < 100)
> echo "rmsd reference mass out rmsd.res.all.0$i.dat :$i nofit"
> @ i++
> end
> while ($i <= $last)
> echo "rmsd reference mass out rmsd.res.all.$i.dat :$i nofit"
> @ i++
> end
>
> echo "EOF"
>
>
>
>
>
> On Wed, Dec 31, 2008 at 2:11 PM, Beale, John <jbeale_at_stlcop.edu> wrote:
>> I need to make a plot of C-alpha RMS deviations (in Angstroms) vs. residue number for a protein that I am studying with MD. Is it possible to do this in ptraj? If so, how do I set it up?
>>
>> John Beale
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