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

Hello, I try to calculate rmds between a pdb file and NAMD coor file.



I obtain value like 1.310232404E-15

Does anyone know where the error is?

From the CHARMM documentation, it appears that the command to read a NAMD file may be

READ NAMD FILE "filename"

As far as I can tell you did not actually read more than one coordinate set. So getting the rmsd between two identical coordinate sets is indeed expected to return zero, within numerical (double) precision.
And I hope you understand that BOMLEV -5 is an absolute No-No if you want to get help ....

In setup.pdb and dynami.1.coor there are : a protein, a ligand in a water box.

I made a simulation setup.pdb is the first frame and dynami.1.coor is the last frame.

The value of rmsd should be between 0 and 3. Here is the value I get 2.581522112E-15

From my readings, Charmm works with main set and comp set but it still doesn't work

Your statement "open read unform ....." only open the file, no reading is done.
Is dynami.1.coor a binary file? It is better to work with formatted coordinate files, either in pdb-format or the charmm format.
To avoid the confusion the obsolete construct with an open statement followe by a read or write should be avoided (open is still necessary in some cases):
read psf card append name setup.psf (I am not sure that xplor is needed)
read coor pdb name setup.pdb
read namd file dynami.1.coor

Note also that
coor copy comp select heavy end
copies coordinates from the main set (which came from setup.pdb) to the comparison set, and that the following RMS calculation is therefore performed on two identical coordinate sets.

Thanks

Indeed dynami.1.coor is a pdb coordinate file, not a binary file, I will remove the obseleted structures

That's what I want to do is to compare the rmsd of the main set with the comparison set, I tried again by adding orient protein before the rms calculation

define heavy select (segid HETE .and. .not. type h*) end
define protein sele type ca end
coor orient rms sele protein end
coor rms select heavy end
set rmsd ?rms

I obtain


CHARMM> coor orient rms select heavy end
SELRPN> 20 atoms have been selected out of 32659
**WARNING** ALL SELECTED COORDINATES UNDEFINED

**** WARNING **** FOR THIS OPERATION, THERE WERE 20 MISSING COORDINATES

This is an outline of what you want to do:
read rtf ...
read param ...
read psf ...
read coor pdb name setup.pdb
read coor pdb name dynami.1.coor COMP
coor orie rms sele type ca end

I have a system containing a ligand (an hetero molecule), a protein (containing amino acids) and a water box

I have realized a simulation of molecular dynamics

I would like to calculate the rsmd between, the coordinates of the ligand in the starting frame (setup.pdb, pdb format) and the coordinates of the ligand in the last frame (dynami.1.coor, pdb format)

read rtf ...
read param ...
read psf ...

read psf card append name setup.psf
read coor pdb name setup.pdb
read coor pdb name dynami.1.coor COMP

define heavy select (segid HETE .and. .not. type h*) end ! For the ligands of the two structures that I want to align

coor orie rms sele heavy end

Prompt :

CHARMM> coor orie rms sele heavy end
SELRPN> 20 atoms have been selected out of 32599
**WARNING** ALL SELECTED COORDINATES UNDEFINED

**** WARNING **** FOR THIS OPERATION, THERE WERE 20 MISSING COORDINATES