[gmx-users] one ligand in ATB

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 6 13:24:25 CET 2012

Hey Ahmet,

The conformation is not important. What is important is that the
number and order of the atoms in you structure match the topology
file. If the order is wrong, you can simply swap lines to make them
match. If the number of atoms is different, you have to fix your
structure to be able to use the topology. Mind not to try and run the
complex through pdb2gmx. Separate the protein and the ligand, running
the protein through pdb2gmx. Then add the ligand to the processed file
and add an #include statement to the topology, pointing to the
molecule topology from the ATB, and add the number of ligands at the
end, under [ molecules ].

Hope it helps,


2012/3/6 ahmet yıldırım <ahmedo047 at gmail.com>:
> Hi,
> I have a pdb file containing only one ligand. There is already .gro and .itp
> files of this ligand at Automated Topology Builder (ATB).
> I want to use the gro and .itp files of this ligand from ATB. The ligand
> coordinates in my pdb file is different than at ATB. i.e. ATB have used
> another coordinates when it obtains .gro and .itp files.
> can I use these files obtained from ATB? If ok, doesn't the
> location/position of the ligand change in the enzyme?
> Greetings
> --
> Ahmet Yıldırım
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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