Re: [AMBER] Error with addIons

From: David Case <>
Date: Tue, 19 Nov 2019 13:14:10 +0000

On Tue, Nov 19, 2019, 조준범 wrote:

>addIons RTIL Li+ 10
>/home/cleartimes24/amber18/bin/teLeap: Fatal Error!
>addIons: Argument #2 is type String must be of type: [unit]

The name of the lithium residue is "LI", not "Li+". This follows the
PDB standard nomenclature. Use the "list" command in tleap (right
before you try the addIons command). That will show you what ions have
been loaded, and are available for use in tleap.

[Aside: the reason that Na+ works is this: originally, developers making
parameters just artbitrarily chose whatever names they liked, with
little thought about standards. Later, when we standardized ion names
to be those that should be used (following standards developed at the
PDB) we also allowed the older "Na+", "K+" and "Cl-" names to be
recognized, to avoid having lots of existing scripts fail. We did not
do that for the much less common LI ion.]

...good luck....dac

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Received on Tue Nov 19 2019 - 05:30:03 PST
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