[gmx-users] Converting multiple crystal structure PDB's into .xtc file

[Michael Carter]

Hi,

I have been trying to convert multiple PDB files into a .xtc file using trjconv. I have saved all the crystal structures into one large PDB (with TER records included). However when I perform the trjconv I obtain a .xtc which consists of one large co-ordinate system (80,000 atoms) rather than 40 representations of 2000 atoms.

Therefore, once I run any further analysis, such as PCA, using a reference PDB file, I obtain an error where I am trying to compare a system of 2000 atoms to the co-ordinates of a system which GROMACS thinks is 80,000 atoms in size.

Is there a solution to writing multiple PDB's to an .xtc so that GROMACS understand that this is a crystal structure trajectory rather than one large system?

Thanks,
Michael


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