[gmx-users] calculating properties of polyaromatics using gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 10 16:14:04 CEST 2007

Hi Fredrik,

Basically, you don't (you can't in any case run it on something not in
the database). pdb2gmx is designed to build topologies for
proteins/dna. There are some more building blocks, and you can add
your own, if required. If you mean polyaromatic in terms of a polymer
of an aromatic building block, you may want to add these blocks to the
appropriate .rtp file to make life easier on you. However, your
biggest problem seems to be to obtain good topologies for your
building blocks in the first place. I'm not sure whether these (e.g.
aniline) are available in GROMOS by default.



On 4/10/07, Fredrik Blomgren <fredrik.blomgren at cit.chalmers.se> wrote:
> Dear All
> I am a new user of Gromacs which means I am in the (somewhat painful)
> process of learning how to use the program. My goal is to calculate
> properties for polyaromatics containing nitrogen and sulfur. I want to use a
> united atom force field and if I have understood it correctly I should be
> able to use Gromos.
> My problem is that I find it hard to get started. I am trying to test the
> program for aniline (benzene with an amino group). I have a pdb-file of the
> molecule and tried to run pdb2gmx which didn´t work because in my pdb-file I
> didn´t specify a residue. This leads to my question: How does one run
> pdb2gmx with a molecule that is not an amino acid residue or something else
> that is stored in the database of Gromacs?
> Best regards
> Fredrik Blomgren
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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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