[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 11 09:27:09 CET 2008


Contrary to Chris, I think it's easier/better to leave the .rtp database for
building blocks of chains (and definitely advocate against bothering with
the file for newbies). Small ligand topologies are better made seperately
"by hand" and inserted in manner similar to the procedure in John Kerrigan's
In any case, for compounds with names like
ACID, I would scratch my head a few times and probably go search for a
different project. It's a charged fairly large, complex small molecule ;)
with everything conjugated, which makes it a daunting task to derive proper
parameters. For example, PRODRG will likely return you a naphtalene ring
with no charges, quite contrary to what you would expect, and which may be
necessary for the interaction with positive charges (a la cation-pi

But these are just my two cEUR (which now is ~ 3 cUSD by the way ;))



On Jan 10, 2008 7:34 PM, Chris Neale <chris.neale at utoronto.ca> wrote:

> When actually building the topology I find it easiest to create the
> residues in the relevant .rtp and allow pdb2gmx to build the topology for
> you. However, all this does is correctly connect everything and put your
> parameters where they should be. All previous comments (in this thread and
> the hundreds of other threads on this topic) still apply about how to come
> up with the parameters... read the original papers and reproduce their
> methodology.
> Chris.
> >Dear users,
> >                 I am working with PTP1B protein. Recently I
> >tried to run it in gromacs along with an inhibitor
> >problem is that  gromacs does not recognize  FNP and hence I
> >am not able to generate a topology file of it using pdb2gmx. I
> >tried using the The Dundee PRODRG server to generate the
> >topology file with the pdb file as the input. The problem is
> >that it does generate the topology file but without any
> >hydrogens. Even the  polar hydrogens information is not
> >available inspite of it being a part of my input pdb file.
> >Thus I am not able to use FNP with the polar hydrogens for my runs.
> >
> >If anyone has faced similar problems please do help if you can.
> >
> >Thanking you,
> >Cheers.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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