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

massimo sandal devicerandom at gmail.com
Mon Aug 19 12:45:54 CEST 2013

Hi Justin,

>> 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.
Well, apparently it fails when it has to deal with some systems, even when
turning energy minimization off. The ligand I'm talking about is
costunolide ( http://en.wikipedia.org/wiki/Costunolide ). Strychnine is
another ligand where it introduces artefacts -in the case of strychnine,
turning energy minimization off is enough to bypass artefacts, but somehow
not for costunolide.

(Let's leave alone the fact that PRODRG ligands are not very well
parametrized for MD, I'm aware of that, but we know it's generally good
enough for our purposes).

>  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).
Okay, so there is no utility that does it already, it seems? If it's matter
of scripting, it's okay, I can do that, but I hoped there was someone who
already had my problem. :)
Can you elaborate a bit more / point to relevant documentation for .itp

thanks a lot,

> -Justin
> --
> ==============================**====================
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
> ==============================**====================
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