[gmx-users] adding ions in Gromacs 4.6.5

Justin Lemkul jalemkul at vt.edu
Tue Nov 18 13:30:48 CET 2014

On 11/18/14 1:47 AM, soumadwip ghosh wrote:
> Dear Justin,
>                     thanks for your reply. I really dont know how to create
> the .itp file from the .pdb file of the TMA cation. Do I need a topology
> builder? After making the .itp file, how should I proceed? If I have to add
> it by genion, then I guess the tma.itp must be a part of the ions.itp file
> of the forcefield directory, right?

You can't add polyatomic ions via genion.  They have to be inserted with genbox 
-ci -nmol (gmx insert-molecules in 5.0).  You need to build the topology 
somehow; for CHARMM I suggest ParamChem.  Amines are well covered in CGenFF and 



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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