Re: [AMBER] Using packmol to produce multiple instances of the same molecule

From: case <>
Date: Sat, 29 Jan 2011 09:55:34 -0500

On Fri, Jan 28, 2011, Maria Pikoula wrote:
> I can construct my carbohydrate molecule in sleap, that's fine. I would
> like to actually end up with multiple instances of that molecule for my
> simulation, neatly packed in a very precise way, and for that I have
> used packmol. In packmol I arrange the molecules plus water and some
> ions, and I end up with a .pdb file with everything in it.
> I then proceed to use that file in sleap again, in order to create
> coordinate and parameter files. That's were things go wrong...and I end
> up with a wrong topology file. Also, when I save the same .pdb file
> through leap, it ends up a bit messy..

Two points:

1. please indicate in email what went wrong -- what was the error message,
etc. I'm glad you gave your input files, but it would take a long time for
someone on the list to try to reproduce the problem, just to find out what the
error was.

2. I'm no packmol expert, but I think you would need to set the box parameters
in the second script. Also, you might try tleap: it tends to be more verbose
and might give some additional clues.


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Received on Sat Jan 29 2011 - 07:00:03 PST
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