Re: [AMBER] cpptraj - rmsd/rmsf & reference structure

From: Daniel Roe <>
Date: Thu, 26 May 2016 07:22:55 -0600


On Thu, May 26, 2016 at 3:19 AM, colvin <> wrote:
> Is this strange bug fixed?
> I am still getting the same problem as described. Currently using CPPTRAJ ver. 15.

That bug is indeed fixed in version 16 (and I recommend upgrading).
However, your problem does not appear to be the same one.

> Does this means that in case 1, the rmsd calculation is not rmsfit to the reference structure? and in case 2, it is rmsfit into the first frame of the input trajectory instead of my reference structure - min2_worst.rst?

In both cases you're specifying 'first', which means use the first
frame read in as the reference structure. You need to specify
'reference' or 'ref <refname>' etc. if you want to use a specific
reference structure. See the manual for full details.

> For the atomicfluct, if rms reference command put before atomicfluct, the calculation will rmsfit to the reference structure, right?

Yes, that is what the 'rms' command does by default unless 'nofit' or
'nomod' is specified.

Hope this helps,


> My input:
> trajin ../combine_traj/
> center :1-400
> image familiar
> reference ../../min2_worst.rst
> rms reference
> atomicfluct out backbonermsfluct_all :1-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_all.arg :1-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_all.gnu :1-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_rec :1-394.C,CA,N,O byres
> atomicfluct out backbonermsfluct_rec.arg :1-394.C,CA,N,O byres
> atomicfluct out backbonermsfluct_rec.gnu :1-394.C,CA,N,O byres
> atomicfluct out backbonermsfluct_pep :395-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_pep.arg :395-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_pep.gnu :395-400.C,CA,N,O byres
> atomicfluct out backbonermsfluct_activesite :395-400<:4.0 byres
> go
> Pls advise.
> Thank you very much!!
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu May 26 2016 - 06:30:03 PDT
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