Hai,
Thank you very much! Indeed, the correct call "leaprc.water.tip3p" fixed the other errors.
The problem is that my fallback call " loadamberparams frcmod.ionsjc_tip3p" was accepted
with a positive feedback, and then addions returned a confusing error message. These two
put together hinted of no problems with ions and water.
Perhaps a change in an error message could be made to give a hint of what's missing.
Thank you again!
Best regards, Voytek Kasprzak
Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer,
Basic Science Program,
Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research (FNLCR)
Frederick, MD 21702
(301) 846 5537
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Hai Nguyen [nhai.qn.gmail.com]
Sent: Tuesday, February 21, 2017 4:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER 16 problem with LEaP's addIons command
Hi,
sorry for the confusion. AMBER16 is indeed different from AMBER14 in tleap
behaviour.
Replace
"source leaprc.tip3p"
by
"source leaprc.water.tip3p"
Hai
On Tue, Feb 21, 2017 at 4:20 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Dear Amber Users,
>
> While testing the combined RNA and DNA FFs in Amber 16 I ran into a
> surprising problem in LEaP
> with addions and solvateBox commands. I though it was an issue with the
> compilation (I do not
> maintain the Amber package), but I was instructed by the administrators
> to pose this question
> on the AMBER forum.
>
> Here is what I did in Amber 16-based LEaP session (comments on the right):
>
> > module load amber - initialize amber 16
> in this set-up)
> > tleap
> >> source leaprc.RNA.OL3
> >> source leaprc.DNA.OL15
> >> source leaprc.tip3p - FAILS, a suggested way to load water and
> monovalent ions params
> > in the A16 manual
> >> loadamberparams frcmod.ionsjc_tip3p - still works
> >> mol=loadpdb RNA-DNA-Hybrid.pdb - load a hybrid RNA/DNA
> structure
> >> check mol - works fine
> >> addions mol Na+ 0 - FAILS with an
> error: Argument #2 is type String
> must be
> of type [unit]
> >> solvateBox mol TIP3PBOX 10.0 0.8 - FAILS with the same error
> message
>
> What fails in Amber 16 works in Amber 14 (as it has for as long as I can
> remember).
> It appears that the variable name mol is all of a sudden misinterpreted,
> even though in the
> "check mol" commands it works fine.
>
> I am perplexed by this new issue and would appreciate any suggestions on
> how to
> dubug and fix it.
>
> Thank you in advance, Voytek Kasprzak
>
> PS. I did not see this message posted after my earlier e-mail, and I am
> sending it again. I apologize
> if for whatever reasons this message ends up being posted twice. Voytek
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 21 2017 - 15:00:02 PST
