[gmx-users] build membrane system from Charmm-Gui

Justin Lemkul jalemkul at vt.edu
Fri Aug 22 22:48:40 CEST 2014

On 8/22/14, 4:36 PM, Xiang Ning wrote:
> Hi All,
> I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add water and ions back to the system? I read the previous solution was to modify [molecules] in top file (add ions and waters information manually), are there any detailed explanation of how to do that?

For the coordinates, just paste the water and ion coordinates back into the 
membrane-only file.  For the topology, indeed all you need to do is modify 
[molecules] in the .top to reflect however many waters and ions there are in the 
reconstructed system.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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