Re: how to have large coordinate values in the "coordinates PDB" file

From: Vermaas, Joshua (
Date: Mon Apr 17 2017 - 14:03:15 CDT

Hi Steve,

Yup. PDB files have restrictions on their coordinates, since its a fixed format. 8 characters total, 3 of which are supposed to allow for things up to a thousandth of an Angstrom precision. 1 more character for the decimal point, and you only have 4 more characters left, so anything more than 9999 or less than -999 isn't representable in the format. The solution is to not use a pdb input. For VMD/NAMD purposes, the js file format is the one you want


Instead of feeding NAMD a pdb input with the starting coordinates, you would use binary files that start running into problems only at really absurd problem sizes.

usePluginIO yes
structure apoa1.js
bincoordinates apoa1.coor

-Josh Vermaas

On 04/17/2017 12:44 PM, Nielsen, Steven wrote:

In the coordinates pdb file (in the namd configuration file)
I want to have z-coordinate values of up to 25000. But the column
width in the pdb format doesn't seem to allow for this. I assume
this is a known issue with a known solution but I can't find anything
in previous posts about this.


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