[gmx-users] Re: Starting configuration for gromacs
Mark.Abraham at anu.edu.au
Fri Mar 28 23:03:09 CET 2008
Luis Javier Alvarez wrote:
> Dear Mark:
> Thanks for your response to my mail on the initial configuration for
> gromacs. Since in your reply you implicitly posed some questions I am
> writing directly to you to ask you something in the hope that it shall
> not bother you.
Please leave gromacs-related correspondence on the list. That way it's
archived for others to find later.
> You mentioned that there is the question of wether or not we have access
> to the right tools to set up the initial configuration for gromacs to
> generate the topology file. In fact we do not have anything specialised.
> We are using what we can get from the internet and if necessary we write
> our own programs. So the question is: what are these right tools?
Various force fields have tools that are suited for topology-generation,
like Antechamber or PRODRG or x2top or pdb2gmx, and your choice of force
field will be connected with the availability of such tools and the
nature of your simulation system.
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