[gmx-users] pdb2gmx -ignh

[Justin Lemkul]

On 5/4/16 5:02 AM, Alexander Alexander wrote:
> Dear GMX user,
>
> As you know, naming the Hydrogen atom differently in different FF and in
> .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met
> the issue when I wanted to convert my self-made (by Avogadro)
> heptapeptide.pdb to heptapeptide.gro file.
>
> I could get rid of them using "-ignh" which is ignoring H atom in the
> heptapeptide.pdb file.Then, If I understood correctly this means no normal
> Hydrogen atom there is in produced heptapeptide.gro file?! If so, do you
> think if this makes sense proceed further with a peptide which is missing
> the normal hydrogen atom in?
>

-ignh does not mean that there are no H in the output, only that H in the input 
are ignored.  pdb2gmx reconstructs missing H using .hdb entries.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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