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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Sep 17 10:25:39 CEST 2014

Hi Michael,

TER is used for ending a chain. Start each pdb file with MODEL and end it
with ENDMDL. Then concatenate the pdb files and then convert.


On Sep 17, 2014 10:22 AM, "Michael Carter" <Michael.Carter at icr.ac.uk> wrote:

> 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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