Hi Ryan,
A couple of things you can try:
1. Make sure you source amber.sh from your installed directory.
2. Run
which rism3d.snglpnt
To see where your computer is finding rism3d.snglpnt.
The treecode options were included with AmberTools19, so if your not seeing those options then you must be accessing a different version somehow.
Tyler
> On May 15, 2019, at 7:45 AM, Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote:
>
> Hi David,
>
> My README does state that I have AmberTools19, and this is my first time
> installing Amber on this computer, so the problem can't be an older version
> coming before AmberTools19 in my path.
>
> So that leave an installation problem? Are the --tree flags dependent on
> some additional library I might not have properly installed?
>
> Also, how new are the --tree flags in the production release? Is it
> possible they were never included or is this definitely an install problem?
>
> And thanks for pointing me in the direction of MoFT. I'll check it out!
>
> Thanks again for your help,
>
> ryan
>
> On Wed, May 15, 2019 at 5:47 AM David A Case <david.case.rutgers.edu> wrote:
>
>> 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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>>
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Received on Wed May 15 2019 - 10:30:03 PDT
