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 - 13:30:03 PST
