[gmx-users] How to build a 20 unit chain of chondroitin 6 sulfate? Help needed!

Justin Lemkul jalemkul at vt.edu
Tue Jan 21 04:39:13 CET 2014

On 1/20/14, 8:15 PM, Libin wrote:
> Hi.
> I have the pdb file of a single unit of chondroitin 6 sulfate and need to
> build a chain consisting of 20 units of the same.
> As I am new to gromacs, i would be glad to get proper directions to do the
> same.

Gromacs has limited capability in terms of constructing molecules in this way. 
One possible method would be to place the monomer, with its principal axis along 
x (editconf -princ) in a box of with correct dimensions such that images would 
be spaced one bond length away (editconf -d as appropriate), then run genconf 
-nbox 20 1 1.  That's about the only Gromacs-centric way of building the 
polymer.  If that doesn't work, you'll likely have to use some other software to 
build it.



Justin A. Lemkul, Ph.D.
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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