[MMTK] clarification on model=calpha

Edvin Fuglebakk edvin.fuglebakk at gmail.com
Mon Mar 16 09:31:23 UTC 2009


Hi.

I was writing a script to check some assumptions  about how the calpha- 
model works, when some unexpected results turned up which I hope you  
might be able to help me understand.

The assumptions I wanted to check:
- MMTK will read the three-letter side-chain codes from pdb-files and  
assign the corresponding masses to the resiude modeled at the alpha- 
carbon position, even if the pdb-file does not contain the coordinates  
of that side chain.
- The normal mode analysis using the CalphaForceField depend only on  
the positions of the alpha carbons and the masses of the corresponding  
residues.
- The normal mode analysis using the DeformationForceField depend only  
on the positions of the alpha carbons.

So I wrote a script to compare the models MMTK genereates from a pdb- 
file, calculate Normal modes and compare the resulting modes.

I ran this script on pdb-files contaning all atom records in the pdb- 
files  and only the alpha carbon records respectively ( grep ^ATOM and  
grep ^ATOM.*CA ).

Regarding the first two assumptions mentioned above:
- I found the masses and positions of the models to be the same for  
both kinds of pdb-files
- I found the normal modes to be somewhat different between the two.


It will be much appreciated if anyone can clarify this (less  
appreciated if it involves pointing out stupid mistakes in my script,  
but appreciated nontheless :-) ).

Attached:
the script and one of the pairs of pdb-files I've tested this on.

-Edvin Fuglebakk

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