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Re: [ESPResSo-users] PDB files
From: |
Peter Košovan |
Subject: |
Re: [ESPResSo-users] PDB files |
Date: |
Mon, 9 Nov 2015 14:55:12 +0100 |
Hi Paul,
The writing of PDB files is a workaround for writing generic particle configurations in a format originally designed for storing coordinates of atoms in proteins. PDB files contain a lot of entries that are not used by Espresso. As far as I have understood, "Fe" is used because iron can have an arbitrary number of bonds, so vmd does not complain if you have a branched structure. In general, vmd tries to guess a number of things from the atom type (its size, colour, number of possible bonds and their length...), so replacing type FE with another element might not lead to the result you desire.
If you want to write your particle coordinates in a format which more closely corresponds to how they are represented in Espresso, I recommend using the vtf/vsf/vcf file format.
Since vtf has been around, I personally consider the use of pdb in Espresso as obsolete. Only a fraction of their content stores information useful for Espresso. The rest is generic data which cannot be omitted because the format relies on a fixed number of characters on a line.
Best,
peter
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