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.
Mark
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