CHARMM Development Project Forums User Discussion & Questions Molecular Dynamics Calculation of rmsd from NAMD coor file

If you go through the READ BEFORE POSTING topic carefully, you will see there are some strong hints about what information to provide if you want assistance trouble-shooting a problem, and how to provide it.

Okk, I read, before I have tried scripts posted here but it did not work

https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=27868
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1050
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=9744

To be quite specific:
The important point is that all you have posted so far is essentially "it does not work". If you want help to solve your problem you have to post enough information for us to help you:

Post brief but complete input/output files
No streaming, no CHARMM variables, no bomlev -5 or the like.
In your most recent post showing some output, you only show the final error message.
What makes you think that there were no errors, or other relevant information earlier in the job? That is quite likely to be the case (why else would CHARMM complain about missing coordinates), hence the requirement for full input/output files.

I use a classical toppar file
The system is 7aeh.pdb : SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957

I use classical toppar.str file and classical toppar folder
In attach:
- r8h.str (the ligand str file)
- setup.psf (the ligand with the protein)

The first frame
- setup.pdb
The last frame
- dynami.1.coor

The script which gives me a 10^15 value for the rmsd
- calculate_rmsd_coor.inp


I added ".txt" at the end of the files to be able to send them but it must be removed

the output

Why do you use the command
"coor copy comp select heavy end"?

You should NOT use bomlev -5.

Since there are numerous messages about missing coordinates when you read dynami.1.coor you have to fix this first. This is your primary problem.

Ok, I will analyze,

Thanks for your advice.

One thing to know is that CHARMM is not very graceful about reading PDB files; it is regarded as an import/export format only, and not a native file type. The Script Archive forum has a number of posts on the topic. Files with multiple segments usually require splitting into one file per segment.

READ COOR PDB takes several options that make it possible to avoid splitting the file: RESI to override residue numbers and instead use RESID and SEGID information. CHAIN <chain id> or SEGI <segi> reads just the lines in the file that contain the specified CHAIN/SEGI information (which may or may not be the same as the PSF SEGI since it is just a filter applied to the reading of the PDB coordinate file). There are also options to use or skip certain lines (HETATOM, ATOM, specified residue names) or to map residue names in the file to names in PSF.

see test/c39test/readpdb.inp for examples. io.info may not be quite up-to-date on these options.

For bomlev -5 : In miscom, paragraph 14,

"-5,-4 Limit exceeded type of errors" this is the only line where I don't see what exceeded type of errors means.

As I'm in the learning phase, it would be a value of -1 that I should put.

In test/c39test/readpdb.inp we call directly the necessary segment when we read the pdb file, interesting