[gmx-users] if PRODRG calculate incorrectly

[Mark Abraham]

On 23/09/2011 4:48 PM, ahmet y?ld?r?m wrote:
> 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.

Yes, this is not an easy thing to do. Modelling an arbitrary organic 
compound is a difficult task. There are links from the link I provided 
last time that will help you.

> 2) Justin 
> tutorial:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> 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 "drg.itp."
> Then how can I generate .gro file using another program?

Again, follow the links, please.

Mark

>
> 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 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     On 17/09/2011 11:28 PM, ahmet y?ld?r?m 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
>
>     Mark
>
>     -- 
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>
> -- 
> Ahmet YILDIRIM
>
>

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