Re: [AMBER] RTIL simulation

From: David A Case <>
Date: Thu, 21 Nov 2013 07:52:47 -0500

On Wed, Nov 20, 2013, Saeed Nasiri wrote:

> I want to do ionic liquids simulation step by step with tutorial in amber
> site. All things go well but in the last part
> "$ tleap -f"
> some errors appears. The leap.log file was attached the email. I would be
> appreciate if you help me with problem?

It looks like you did not follow the instructions in Section 2.2 (about
editing the mol2 file). [This is needed because antechamber does
not handle boron compounds.] Please note especially section 2.3, where you
can examine your bf4.mol2 file, and can compare it to a "good" one.

> and one more thing about antechamber: this utility can not do analyze
> charge for molecules or ions?

Please see the andtechamber section of the users' manual, and/or read section
2.1 of the tutorial, where instructions for handling ions are described.
Experiment with your inputs until you can mol2 files that match the ones
provided in the tutorial.

...good luck...dac

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Received on Thu Nov 21 2013 - 05:00:04 PST
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