[gmx-users] Non integer charge value

Justin Lemkul jalemkul at vt.edu
Thu May 10 14:36:51 CEST 2018

On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> Hi all,
> I have added a non standard amino acid 'Hydroxyproline' to my forcefield
> (from literature) Charmm27 and after using pdb2gmx i could see that the
> system has a non integer charge value for 1 protein chain out of 3 protein
> chains.  (All 3 chains contain the non standard amino acid)
>   The problem is occuring in the chain in which the terminal residue is this
> hydroxyproline. (All other places where the 'HYP' residue appears, the
> charge is 0). I tried using different terminii just to be sure that the
> problem is not because of the terminii.
> What should be done in such a case?

That depends on if the magnitude of the charge is meaningful or not. If 
you have two "correct" chains and one "incorrect" chain, that suggests 
that nothing is likely wrong with your HYP residue so things should be 
fine, but refer to 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be 
sure. The current version of GROMACS (2018.1) handles these rounding 
issues better to trigger fewer false warnings.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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