Re: [AMBER] cpptraj align using the same numbering

From: Martin Rosellen <>
Date: Wed, 16 Jun 2021 18:05:42 +0200

Sorry for that. Here is the cpptraj commands to calculate RMSD values of hairpins:

parm native_hex.prmtop
trajin native_hex.inpcrd
trajin productions/

strip :WAT,Cl-
strip .H*

align :1-1332.CA&!:2-12,223-233,444-454,665-675,886-896,1107-1117

rmsd :2-12.CA out body_aligned/rmsd_hairpin_1.dat nofit

rmsd :223-233.CA out body_aligned/rmsd_hairpin_2.dat nofit

rmsd :444-454.CA out body_aligned/rmsd_hairpin_3.dat nofit

rmsd :665-675.CA out body_aligned/rmsd_hairpin_4.dat nofit

rmsd :886-896.CA out body_aligned/rmsd_hairpin_5.dat nofit

rmsd :1107-1117.CA out body_aligned/rmsd_hairpin_6.dat nofit

It is clear to me now that if the hexamer would have been rotated for the best fit by the ‘align’ command then all the RMSD values of the hairpins would be really high. Still, is it possible that the hexamer is rotated by ‘align’ for the best fit?


> On 16. Jun 2021, at 15:23, Daniel Roe <> wrote:
> Hi,
> On Wed, Jun 16, 2021 at 8:55 AM David A Case <> wrote:
>> On Wed, Jun 16, 2021, Martin Rosellen wrote:
>>> I run a simulation of a hexamer and want to calculate RMSD values of
>>> hairpins found in each monomer. For that I want to align the protein
>>> body. When I aligned the first two frames in Chimera,
>> You don't say what command you used to do the alignment in Chimera, or, for
>> that matter, what commands you using in cpptraj. The latter would not place
>> monomer 3 on top of monomer 1 unless you had some specific arguments that
>> requested that.
> As Dave said, it would be best to post the actual input you tried, and
> if you didn't get the result you expected something we (I) could use
> to reproduce the issue (topology, coords, input, etc).
>> [Aside-- Dan, the description of the 'align' command in the manual is
>> circular: it just says that the 'align' command "aligns the structure". What
>> is the difference between this and 'rms'?]
> The 'align' command is just a bare-bones implementation of best-fit
> 'rms' without creating a data set or any other functionality like
> per-residue rms calc. etc. Guess I should be more clear in the manual
> (boy if I had a nickel for every time I said that...).
> -Dan
>> .....dac
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Received on Wed Jun 16 2021 - 09:30:05 PDT
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