[gmx-developers] pdb files are mutilated by I/O routines

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 7 14:48:49 CEST 2020

GROMACS does some things under the hood when reading and writing pdb 
files. One issue is that it changes hydrogen names, another that it 
changes chain labels. I have submitted a patch for the first issue, or 
actually two.

1) where I introduce flags that allow to turn this behavior off, that 
means more parameter passing and new command line arguments for some 

2) where I removed the functionality alltogether. In this case quite a 
few tests are affected. 

Opinions, suggestions?
David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.

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