[gmx-users] Heavy Hydrogens

Justin Lemkul jalemkul at vt.edu
Thu Apr 23 23:39:32 CEST 2015

On 4/23/15 4:25 PM, Matthew Harrigan wrote:
> Hi all,
> There is an option in pdb2gmx "-heavyh" which shuffles some mass from the connected heavy atom to the hydrogen. I want to do this, but starting from a top, gro pair of files. Specifically, I don't want gromacs to try to regenerate all the forcefield parameters in my top file. Does anyone have suggestions for how I can go about this?

Write a simple parser that modifies the listed masses in [atoms].  This should 
be straightforward in something like Perl or Python.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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