I want to create topology files for an arbitrary molecule that is not included in gromacs forcefield entry. Which software or code can I use?

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Amir Abbasi

thanks Stephane. Is AmberTools a good software to creating this molecule topology file?

yes I want to simulate a graphene oxide sheet in gromacs. but there is a code to convert amber topology files to gromacs topology files. if i can't create .top file directly ican create it with Ambertools then convert it.

George Fitzgerald

Try openbabel. It supports many file formats

http://openbabel.org/wiki/Main_Page