Re: [AMBER] converting gromacs topology to amber

From: Daniel Roe <>
Date: Mon, 3 May 2021 08:57:36 -0400


On Sun, May 2, 2021 at 12:32 PM Ayesha Fatima <> wrote:
> I also tried using cpptraj but it also throws me the error of
> *Molecule NLU1 is not defined in gromacs topology.*

First, I really don't recommend using cpptraj to do topology
conversions. Cpptraj is really only intended for trajectory/data
analysis; it has *not* been vetted at all for converting parameters
between different formats.

Second, by default cpptraj will look for gromacs topology data (that
is not in the same directory) in the directory defined by the GMXDATA
environment variable; specifically, it expects things to be in the
"$GMXDATA/top" directory. I just realized this is not documented

Hope this helps,


> NLU1 is the ligand
> is the ligand.itp required or gro file required
> thanks you
> Ayesha Fatima
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Received on Mon May 03 2021 - 06:00:10 PDT
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