[gmx-users] Question on generating hydrogens

Justin Lemkul jalemkul at vt.edu
Mon Apr 29 14:18:34 CEST 2019

On 4/22/19 5:39 PM, tca1 wrote:
> 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 
> creation.
> 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.

The principal function of pdb2gmx is to produce a topology. Production 
of a force field-compatible structure is actually somewhat of a side 
effect. The only way to prevent the production of a topology is to 
explicitly disable these functions in the code and recompile.



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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