[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

Justin Lemkul jalemkul at vt.edu
Sun Aug 18 21:59:15 CEST 2013

On 8/18/13 3:37 PM, massimo sandal wrote:
> Hi,
> I have a small ligand that apparently PRODRG gets wrong -it completely
> alters the structure, borks angles etc. making it not what we want. So I
> used xplo2d to obtain a suitable set of files that I used for docking (with

Interesting.  The hallmark of the PRODRG development process was that bonded 
geometries were very well maintained.  I have never seen such a problem; the 
issues were always with the charges.

> Now, it seems to me that xplo2d does not output a Gromos ff -compatible
> .itp file as PRODRG does. However it produces a CNS .top file, which seems
> to contain most of the same information ( charges, dihedrals, masses etc.)
> Is there a way to convert between the two?

Yes, but it will involve using multiple files.  The CNS topology should be 
reasonably straightforward to parse with, e.g. Perl, but you will have to 
cross-reference bonded parameters from ffbonded.itp by atom type and somehow 
assign charge groups (although that can be done manually after the fact, if needed).



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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