Hi
I agree with your suggestion. (It took time for me to figure out too.)
Hai
> On Feb 21, 2017, at 5:58 PM, Kasprzak, Wojciech (NIH/NCI) [C] <kasprzaw.mail.nih.gov> wrote:
>
> 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 - 15:30:02 PST
