Re: [AMBER] [ Files for Tutorial 32 (Deriving bonded parameters with mdgx)]

From: David Cerutti <>
Date: Fri, 3 May 2019 11:30:40 -0400

If you look in the tarballs for conformations of each molecule you'll find

There are PDB files for many conformations, complete with annotations
showing what Amber NMR restraints would be necessary were you to run sander
to arrive at that same local minimum. There are also "initial guess"
topologies and prepi files--starting points for your force field
development based on gas phase charges that might be created by hand, that
will serve as guides for tleap and other amber programs. One thing I don't
seem to have in there is an Amber inpcrd format file for each molecule, but
you can generate that yourself from one of the PDBs and the prepin files
with tleap, or by taking the given topologies and using cpptraj to convert
one frame of the trajectories in this tarball to Amber restart format:

I didn't expect you to run all the ORCA calculations yourself, so I opted
to just show you how the mdgx &configs and &speval modules work. The
results needed for the next step are provided so that you can get straight
to the data fitting part.

I'm still due to make some updates to the website based on MPS results with
pmemd, and there's a big new patch to mdgx coming soon, just didn't make it
in time for AmberTools19. I'll see about improving this tutorial with that


On Fri, May 3, 2019 at 9:41 AM David A Case <> wrote:

> ----- Forwarded message from Michiel de Hoon <> -----
> Date: Fri, 3 May 2019 09:26:58 +0000 (UTC)
> From: Michiel de Hoon <>
> To: "" <>
> Subject: [AMBER] Files for Tutorial 32 (Deriving bonded parameters with
> mdgx)
> Hello,
> To run the example for MPD (methyl(2,4)-pentanediol) in Amber tutorial 32
> (Deriving bonded parameters with mdgx), isn't the PDB or coordinate file
> for MPD required?I couldn't find links to these files from the tutorial.
> Thanks,-Michiel
> _______________________________________________
> AMBER mailing list
> ----- End forwarded message -----
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Received on Fri May 03 2019 - 09:00:02 PDT
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