So, I need to get the mol2 file(new) from old one using gaff atomtypes. Is it correct what I am saying?
Get Outlook for Android<
https://aka.ms/AAb9ysg>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Monday, January 10, 2022 7:44:12 PM
To: AMBER Mailing List <amber.ambermd.org>
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.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 10 2022 - 07:00:03 PST
