[gmx-users] Question on generating hydrogens

tca1 tca1 at rice.edu
Mon Apr 22 23:39:18 CEST 2019

Hi all,

Is it possible to use pdb2gmx to generate hydrogens for a  
configuration file without also creating a topology file? Based on the  
documentation, it seems I can only rename this file, not prevent its  

Ideally, I'd like to prevent this, because I have many  
identically-structured polymer molecules and building the topology for  
the whole system takes a very long time, but I can use a template  
topology file which includes a single-chain itp file and then just  
tells the code how many chains are present (analogously to how  
solvents are handled). However, my initial input file doesn't have the  
hydrogens included, so I've been forced to use pdb2gmx to handle this  
part. I'd love to be able to decouple the steps, though.

Tom Allen

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