Re: [AMBER] Crashed dynamics : connectivity

From: David A Case <>
Date: Wed, 15 May 2019 10:50:27 -0400

On Wed, May 15, 2019, emanuele falbo wrote:
>I am dealing with ion pairing phenomena, and for this reason I am
>simulating a charged inorganic complex bound to cations (Li+, Na+, and
>etc). I get the optimized structure from QM calculations and I use obabel
>in order to convert it to mol2
>obabel -ixyz -omol2 output.mol2
> and then I only use output.mol2 for generating topology and coordinates,

Can you say (a) exactly how you did this step? (b) what is in the mol2
file? The mol2 file should have a single molecule, not a molecule plus
extra cations. Also, if it is indeed "inorganic", there is no standard
way to create topology and coordinates in Amber. So, we need to know
exactly how you did that.

>May it be because the bespoke made frcmod.file does not contain any info
>about Li-M ( M molecules) terms?

If you have a "nonbonded" description of the cations (which is certainly
the expected case for things like Li+ and Na+, then there won't be any
bonds expected -- all the interactions are assumed to be described by
electrostatic and Lennard-Jones interactions.

....hope this helps...dac

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Received on Wed May 15 2019 - 08:00:03 PDT
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