[gmx-users] Conversion of a Gromacs (sub)system to mol2 ?

Cesar Lopez inmuno_cl at yahoo.com
Mon Nov 29 16:22:38 CET 2004

Maybe you can try using VEGA, the software uses .gro files and can save them as mol2 format. If you want you can use MOL2MOL. It is othe software that use the sybilmol2 format.

Marc Baaden <baaden at smplinux.de> wrote:


I would like to convert part of a simulation system (ATP to be exact)
to the mol2 format to be able to feed it into another program requiring
that input format.

I have seen that there was a feed on the mailing list about eventual mol2
support, but it is not quite clear to me whether anybody has given it a

So what I'm asking for is whether there is any "working" pipeline to get
from a gromacs system (eg PDB, GRO, ITP..) to a corresponding mol2 format.
I have tried babel, which produces some mol2 file - in a black box way -
which is not properly recognised by the program I want to work with.
So I guess what I'd need is to be able to tell the converter some atom type

Thanks in advance for any hints,
Marc Baaden
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