Re: [AMBER] Help with solvating organic molecule with input .prmtop file

From: Andy Ballard <>
Date: Thu, 1 Mar 2012 12:28:23 -0500

> A possible alternative to "top2ff" is -- is that program
> in your $AMBERHOME/bin? I can't remember if it was released with
> AmberTools 1.5 or not. If so, will dump a force field
> file with _every_ parameter in your prmtop file (including all of your VDW
> parameters), something I don't think top2ff does. will also
> dump a full frcmod and full OFF file with every parameter and residue in
> your system if you want to use that. You can then load this back into
> tleap (after sourcing any other force fields) to override any previous
> force field definitions.
> If it's not present, you'll have to use top2ff, although there will be more
> options in the upcoming AmberTools release.

I've tried using top2ff, and it gets most things right, but not all.

It sounds like is the program I need, but unfortunately
its not in my $AMBERHOME/bin directory. Is there somewhere I could
download it, or does it have dependencies etc. that my current amber
version wouldn't support?

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Received on Thu Mar 01 2012 - 09:30:02 PST
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