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

Justin Lemkul jalemkul at vt.edu
Tue Sep 8 14:24:37 CEST 2020

I am in favor of removing the renaming function altogether. It 
completely breaks things for our polarizable model, too. Nuking it would 
make everything work more smoothly and would allow me to de-complicate 
the code that I've been working on.


On 9/7/20 8:48 AM, David van der Spoel wrote:
> 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 
> programs.
> 2) where I removed the functionality alltogether. In this case quite a 
> few tests are affected. 
> https://gitlab.com/gromacs/gromacs/-/merge_requests/489
> Opinions, suggestions?


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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