Re: [AMBER] GROMACS to AMBER .top and .pdb conversion using gromber

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 9 Sep 2019 11:57:50 -0400

A recent update should add more helpful error messages.

That said, the 'chamber' command will convert from CHARMM format to Amber.
I'd recommend using that option instead of gromber if you start with
CHARMM-GUI.

HTH,
Jason

On Sat, Jul 6, 2019 at 7:57 AM cpimenta <cpimenta.itqb.unl.pt> wrote:

> Hello,
>
> I used charmm-gui to assemble a bilayer membrane with charmm36 and ran
> the protein/membrane system with water and ions for 100ns using
> gromacs-2019.1. I tried using gromber to convert the topology and
> structure files to amber format using the processed topology and setting
> "topdir" but parmed (Version 3.2.0) returns "Action gromber failed
> ParameterError: Not all angle parameters found"
>
> Is it possible to have parmed printing the cases that lead to the error?
>
> Since the membrane was assebled in charmm-gui, charmm36ff files were
> downloaded from MacKerell lab webpage and I was able to run MD,
> shouldn't all parameters be in the topology?
>
> Will gromber convert to Amber format (using the same FF) or will it
> convert to AmberFF?
>
> Many thanks,
> C├ęsar
>
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-- 
Jason M. Swails
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Received on Mon Sep 09 2019 - 09:00:03 PDT
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