Re: [AMBER] How to generate mol2 file with topology and crd file?

From: Daniel Roe <>
Date: Wed, 1 Dec 2021 11:10:34 -0500


You can use cpptraj do do this:

cpptraj -p <topology file> -y <restart file> -x myfile.mol2

or use the input

parm <topology file>
trajin <restart file>
trajout myfile.mol2

If you need the SYBYL types you should specify the
sybyltype/sybylatom/sybylbond keyword(s) with either the '-xa' command
line arg or as keywords to 'trajout'. See the manual for full details.
Hope this helps,


On Wed, Nov 10, 2021 at 4:26 AM Eugene huh <> wrote:
> Dear AMBER users,
> I'd like to generate lib, frcmod to generate mol2 file with only topology
> and rst file.
> I found 'top2mol2' on the Antechamber page (
> and tried to run 'top2mol2' like
> 'antechamber'. But it didn't work. (See, using AMBER16 and 20)
> How can I use "top2mol2" or is there a better way to create a lib with rst
> and top?
> Best regards
> Eugene
> ᐧ
> _______________________________________________
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Received on Wed Dec 01 2021 - 08:30:03 PST
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