[gmx-users] if PRODRG calculate incorrectly

ahmet yıldırım ahmedo047 at gmail.com
Fri Sep 23 08:48:01 CEST 2011

Dear users,

If I obtain/generate the topology file for a ligand using another program
(except PRODRG);

1) How can I arrange .itp file? Because it seems very complicate.
2) Justin tutorial:
We will make use of two files that PRODRG gives us. Save the output of the
field "The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)" into
a text file called "jz4.gro" and "The GROMACS topology" into a file called
Then how can I generate .gro file using another program?

I was obtaining .gro and .itp files using PRODRG but PRODRG is giving
improper results/output.

best regards

2011/9/17 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 17/09/2011 11:28 PM, ahmet yıldırım wrote:
>> Dear Tsjerk and Justin,
>> Thanks for your reply. I will contact the PRODRG developers.
>> can you suggest anyway/anytool for generating ligand
>> coordinates/topologies?
> http://www.gromacs.org/**Documentation/How-tos/Steps_**
> to_Perform_a_Simulation<http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation>
> Mark
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