Re: [AMBER] 3D-RISM options

From: David A Case <>
Date: Wed, 15 May 2019 08:46:55 -0400

On Tue, May 14, 2019, Ryan Pavlovicz wrote:
>I believe I have the most up-to-date version of AmberTools, since I just
>downloaded and installed it last week (although I get an 'amber18'
>directory when I decompress the download.) Additionally, when I run
>update_amber --upgrade, I see that "No major upgrade available".

AmberTools19 should indeed be inside an "amber18" folder. To tell what
version you have, look at the top line of the README file in your
AMBERHOME directory. It should say this:

  "This directory tree contains AmberTools19 and (optionally) Amber18."

It is indeed true that the "-h" and "--help" options are not recognized
by the current version of rism3d.snglpnt. However, (as I think you
found out) if you just type "rism3d.snglpnt" with no arguments, you get
the complete option list.

If you are not seeing --tree* options, but do have AmberTools19, then it
sounds like something went wrong during the installation. Or, is it
possible your PATH actually has older version of AmberTools first?
Do some exploring to see what might be going on.

Aside: if you are interested in placing waters or ions based on 3D-RISM,
you may be interested in MoFT, which is new in AmberTools19, and offers
a different way to do this placement. See Chapter 37 of the Amber 2019
Reference Manual. I'm cc-ing this to George Giambasu, its author, since
we need to come up with a more detailed tutorial about this. The goal
is to have an improved version of placevent, but you will certainly want
to compare the two options on your systems to see how well we have
reached that goal.

...good luck....dac

p.s.: I'm working on a update patch for the failure of rism3d.snglpnt to
recognize the "--help" keyword.

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Received on Wed May 15 2019 - 06:30:05 PDT
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