[AMBER] How to use GAFF2?

From: Alexander Izvorski <aizvorski.gmail.com>
Date: Wed, 2 Dec 2020 17:41:08 -0800

Dear Amber users,

I'm trying to figure out how to use GAFF2 in antechamber/tleap. It seems
the default for a lot of tools is GAFF (the old version, not GAFF2), and
the options to switch to GAFF2 consistently are not completely obvious.
I'm using ambertools-20.9 from conda-forge.

Here's what I have so far:

1. Run antechamber: no special options needed for GAFF2?

antechamber -i lig_in.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -rn LIG

I noticed that "-at gaff2" is a possible option here - is it needed? If
that is added, what happens is a bunch of errors when running tleap later,
"Error! Could not find bond parameter for: ns - ca" and similar, about a
dozen total for the example molecule, and "Warning! There are missing
parameters." But the frcmod file doesn't seem to have any errors.

2. Run parmchk: "-s gaff2" enables GAFF2 here

parmchk2 -i lig.mol2 -f mol2 -o lig.frcmod -s gaff2

3. Run tleap: source leaprc.gaff2 loads GAFF2

tleap -f tleap.in, where tleap.in is the following file:

source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff2
LIG = loadmol2 lig.mol2
check LIG
loadamberparams lig.frcmod
saveoff LIG lig.lib
saveamberparm LIG lig.prmtop lig.inpcrd

This works using sustiva.mol2
<http://ambermd.org/tutorials/basic/tutorial4b/files/sustiva.mol2> from the
tutorial <http://ambermd.org/tutorials/basic/tutorial4b/index.html> as the
input ligand.

Could someone who is familiar with the options for GAFF2 please have a look
and see if anything is missing from the above?

Best regards,
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Received on Wed Dec 02 2020 - 18:00:02 PST
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