Re: [AMBER] regading no tortion terms

Date: Mon, 10 Jan 2022 14:29:42 +0000

So, I need to get the mol2 file(new) from old one using gaff atomtypes. Is it correct what I am saying?

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From: David A Case <>
Sent: Monday, January 10, 2022 7:44:12 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] regading no tortion terms

On Mon, Jan 10, 2022, MIRA JHAWAR wrote:

>these are my mol2 file of organic molecule and frcmod file

Your mol2 file, and (presumably) the ./morin_sybyl_gaff.prepc that you are
actually using for your tleap runs, don't have gaff2 atom types. Did you
actually run antechamber, and not just parmchk2?

I have to guess here a lot about what you did, but here's what it looks
like: You did a Gaussian geometry optimization, got a mol2 file from
Gaussview, and tried to feed that to parmchk2. This won't work. You need
to start with the GaussView mol2 file, go through antechamber to get a mol2
file with gaff atom types. Then feed that into parmchk2.

If the "morin_sybyl_gaff.prepc" indeed has Sybyl atom types (as its name
suggests), it is not of much use for anything related to Amber.
And the frcmod file you have is also badly flawed; I'd delete it so you
won't accidentally use it later.

Don't neglect to investigate the long bond lengths reported by tleap.

Apologies if I my guess about what you did is wrong.


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