Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method

From: Jason Swails <>
Date: Mon, 8 Oct 2012 23:26:44 +0200

On Mon, Oct 8, 2012 at 9:48 PM, "Γιώργος Λαμπρινίδης" <> wrote:

> Dear users,
> I was trying to run a simulation according to Tutorial A11 (Pyranose ring
> puckering)
> When I finish the "finer" run using Implicit solvent i get a restart file,
> containing the final velocities. In order to create the explicit solvent
> job i transform prmtop and inpcrd files to pdb and I use tleap to create
> the solvated files and i export them. With this procedure I loose all
> velocities, so when i try to run the "flooding" procedure using the mdin
> file from the tutorial i get an error "no velocities found", because of
> the "irest =1, ntx =5" command.
> How can overcome this error? Propably i am missing something.
> In the tutorial how from the restart file of implicit solvent someone goes
> to "flooding" using explicit water?

The input and output files are bundled in a tarball included as a download
at the top of the tutorial. I would suggest looking through this to try
and find your answer (presumably these input files still work, though I
doubt they've been tested recently).

Unfortunately, the NCSU capabilities have rather fallen out of maintenance
and widespread use, at least among the developers, so getting a more
helpful response may take a long wait (if it comes at all). Your best
friends in this case are likely the input files provided on the website and
the manual.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Oct 08 2012 - 14:30:03 PDT
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