Hello,
I would like to analyze hydrogen bonds from some trajectories, using
MDAnalysis and the original PDB that was used to generate CRD and TOP
files. The bonds are between a protein and a peptide.
In the original input PDB file, they are of two different chains. I also
notice that PDB also issues an index number to any TER records it has. I am
worried that when the PDB file is translated into TOP, TER records are
ignored, particles take the atom indexes of TER and hence the index
numbering scheme of TOP will be different from PDB. And it seems that TOP
files don't store chain IDs. The consequence is that when I want to select
the chains in the PDB files corresponding to the protein and the peptide,
the selection would not follow the index scheme of XTC files, which are
derived from the scheme of the TOP files.
Is there a workaround for this? Can I use the PDB file generated by
pdb4amber (it retains chain IDs) or packmol-memgen (no chain IDs) instead?
Best regards,
--
*Lê Thanh Hòa (Mr.)*
*Graduate student at International University, Vietnam National University *
*Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam*
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Received on Fri May 16 2025 - 04:30:02 PDT
