[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:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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