Hello,
I have a suggestion, why don't you try building your HOME-MADE molecules using
PRODRG webserver, it is specially for protein-related molecules, but such
structure like those involving hydrocarbon chains can be made by this
webserver. This server provide topologies for GROMACS.
Good luck with your research!
Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA
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