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

[Justin Lemkul]

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
> HADDOCK).
>

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

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

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