Hi,
As the warning message states, for the 'rms' command to work you need
to select the same number of atoms in your target and reference
structures. For the given mask (:1-249) it appears that your reference
structure has far fewer atoms selected (738) than your target
structure (4059), so you need to either modify the mask expression so
that only the atoms the target and reference have in common are
selected, or use a reference that matches the target.
Also, I highly recommend upgrading to at least the AmberTools 17
version of cpptraj. The Amber14 version is about 4 years old.
-Dan
On Thu, Feb 1, 2018 at 5:26 AM, Manjula Saravanan <manjusimba.gmail.com> wrote:
> Dear Sir/Madam,
> I am trying to run rmsd.dat file for my ligand-protein complex using
> cpptraj in AMBER14. I found the following error is coming every time, so
> that I cant get my rmsd.dat file.
>
> *ACTION SETUP FOR PARM 'com_solv.top' (1 actions):*
> * 0: [rms reference out rmsd_MUT.dat :1-249 .N,CA,C time 10.00]*
> * Target mask: [:1-249](4059)*
> *Warning: Number of atoms in target mask (4059) does not equal*
> *Warning: number of atoms in reference mask (738).*
> *Warning: Setup failed for [rms reference out rmsd_MUT.dat :1-249 .N,CA,C
> time 10.00]: Skipping*
> I am using the input file,
> *trajin prod.mdcrd*
> *trajin prod1.mdcrd*
> *trajin prod2.mdcrd*
> *trajin prod3.mdcrd*
> *reference heat.rst*
> *rms reference out rmsd_MUT.dat :1-249 .N,CA,C time 10.00*
>
> I am attaching the progress.log for your reference. Kindly help me to sort
> out the problem.
> Thanking You
>
> *With Best Regards*
> *S. Manjula*
> *Research Scholar*
> *Laboratory of Biocrystallography and Computational Molecular Biology*
> *Department of Physics*
> *Periyar University*
> *Salem-11*
> *Tamilnadu*
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 01 2018 - 06:00:02 PST
