Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP

From: David A Case <>
Date: Thu, 12 Nov 2015 07:42:49 -0500

On Thu, Nov 12, 2015, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 wrote:

> *> loadoff ions94.lib*

Ooooh...this is way way old. The "modern" leaprc files in Amber load
atomic_ions.lib. Depending on what leaprc file you used for your protein
(leaprc.ff14SB is generally the best choice, but see the manual for more
details), atomic_ions.lib would have been already loaded. By loading
ions94.lib afterwards, you are replacing the current/correct ion descriptions
with ones that are more than 20 years old.

Bottom line: don't load ions94.lib.

[Developers: we "hide" old leaprc files in an oldff subdirectory, but don't do
the same for library or parameter files. There would be some work involved in
doing this, but it would probably help users avoid problems like this.]


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Received on Thu Nov 12 2015 - 05:00:05 PST
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