百毒不侵√,
your input line with the rms command contains an error:
You specified :24-39 as residues for RMSD calculation, and
:24-39,55-69,94-102 as reference for that calculation. Since the number
of atoms in the first and the second set obviously differs, cpptraj
complains about that ("Number of atoms in target mask (64) does not
equal number of atoms in reference mask (160)"): how should cpptraj
compute the RMSD between two structrues, one with 64 and the other with
160 atoms?
You need a pairwise correspondence between the two masks, because the
RMSD is calculated between the respective atoms.
Thus, correct the input line so that the same number of atoms occurs in
both masks.
Maybe that helps.
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 10.12.2024 um 05:22 schrieb 百毒不侵√ via AMBER:
> Professor,
> I want to know how I can calculate rmsd for different residue ranges via amber cpptraj.
>
>
> The following is my input file:
>
>
> parm rec_avg.pdb
> trajin rec_avg.pdb
> parm com_avg.pdb
> trajin com_avg.pdb
> rms rmsd1 :24-39.CA,C,N,O :24-39,55-69,94-102.CA,C,N,O out rmsd_global.dat
>
>
>
> The reference pdb is the second file,com...
> There are always errors:
> Warning: Number of atoms in target mask (64) does not equal number of atoms in reference mask (160).
> Warning: Setup incomplete for [rms]: Skipping
>
> Warning: Set 'rmsd1' contains no data.
> Warning: File 'rmsd_global_1C.dat' has no sets containing data.
>
>
>
>
>
> 百毒不侵√
> 3121063212.qq.com
>
>
>
>
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Received on Tue Dec 10 2024 - 04:00:02 PST
