[gmx-users] trjconv -conect

Justin A. Lemkul jalemkul at vt.edu
Sun May 27 23:47:27 CEST 2012

On 5/27/12 5:26 PM, vijaya subramanian wrote:
> Hi
> Yes, I do have gromacs xtc files. I don't know how to use the .tpr files in
> conjunction with .xtc files which don't have the whole system in them (all atoms)
> ie. if I have an xtc file without the solvent or an xtc file which is filtered
> along on eigenvector when doing pca -has only calpha atoms. trjconv always says
> number of atoms don't match even when I pick the appropriate option from the
> index list.

OK, now I understand - you ran a simulation with more atoms, solvent, etc. and 
now you are trying to visualize the output in terms of only CA atoms.  A .tpr 
file (or even a subset .tpr file created by tpbconv) will not contain the 
information you're looking for and thus the manual solution (writing CONECT 
records in the .pdb file yourself in a text editor) seems to be the only way 
forward in this case.

The advice that the -conect option can be useful for CG systems is true, but 
only in the case that you want to write CONECT records for all CG atoms (which 
would be present in a topology, and thus .tpr file created from said topology). 
  In your case, you are parsing out atoms from some other representation, which 
is not the same thing.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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