[gmx-users] pdb2gmx and the terminal residue

Justin Lemkul jalemkul at vt.edu
Sat Apr 25 17:00:21 CEST 2015

On 4/25/15 10:49 AM, Brett wrote:
> Dear All,
> For the pdb2gmx, if I will not assign charges to the N-terminal residue and C-terminal residue, I need to use pdb2gmx -ter, or I need to use pdb2gmx -[no]ter?

The -ter option allows you to choose protonation state or no terminal processing 
if there are caps.

> In addition, whether there will be charges at the  N-terminal residue and C-terminal residue has relation with the force field used,  am I right?

I don't understand this question.  The individual partial charges on the atoms 
are indeed a function of the force field, but the choice of protonation state or 
capping is totally independent of the force field and is dictated by biological 



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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