[gmx-users] Fitting when structure and reference are slightly different

Jochen Hub jhub at gwdg.de
Wed Jul 9 08:57:20 CEST 2008


I run frequently into the problem that I want to fit a structure on a 
reference which is, however, not completely identical to the structure. 
The reference could, e.g., have a different protonation state or have an 
additional residue at a terminal. Is such a case a backbone-fit using 
trjconv gets erroneous since the atomic numbers of the backbone atoms in 
the two structures are not the same.

The best solution would be the possiblity to give trjconv 2 index files, 
one giving the N fit atoms of the reference and the other the N related 
atoms (but with different atom numbers) of the fitted structure. As far 
as I know, something like that is not supported by gromacs so far, right?

How do you usually deal with such a problem? Is there some more or less 
easy workaround?

By the way, removing the atoms that do not agree in the two structures 
is not an option since I want to start a simulation from the fitted 

Thanks a lot,

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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