Jason and dac,
Thanks for you replies. I usually get the email digest so I take half a day before replying.
>From what both of you mention now I understand that naming a user-generated library atomic_ions.lib (in my case, containing only zinc) will lead to trouble when tleap executes source leaprc.ff12SB.And yes, when I use my script the way it is, the atomic_ions.lib in the $AMBERHOME gets ignored and CL (or NA or K) are no longer seen when using the list command.That is what is happening. I guess I should NOT name my file atomic_ions.lib. I did not post the message because it was very uninformative:
addIons: Argument #2 is type String must be of type: [unit]
addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_Adds counterions in a shell around _unit_ using a Coulombic potentialon a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must beopposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,the specified numbers of _ion1_ [_ion2_] are added [in alternating order].If solvent is present, it is ignored in the charge and steric calculations,and if an ion has a steric conflict with a solvent molecule, the ion ismoved to the center of said molecule, and the latter is deleted....
It was until I read about similar proteins that I realized that my user-generated file was the source of the problem. But I did not know why is automatically loaded. Now it makes sense.
Then, it is a feature, right?
Maybe a warning should be added in the tutorial?
Best regards
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Received on Tue Jun 02 2015 - 14:00:02 PDT
