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
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Received on Tue Feb 21 2017 - 13:30:02 PST
