On 8/19/13 6:45 AM, massimo sandal wrote:
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
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.
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
files?
An .itp is just a topology, so it's identical to a .top except that it does not
have system-level directives and does not #include a parent force field. Manual
sections 5.7.1 and 5.7.2 describe the relevant contents.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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