Re: [AMBER] azobenzene atoms name in amber format

From: Aashish Bhatt <>
Date: Thu, 10 Sep 2020 16:44:30 +0530

Dear Sir

I using the Gaussian output file. I already send the Gaussian output file
and PDB but due to the file size, it was not delivered.
I am using the command.
*antechamber -i mk-pop.log -fi gout -o aza-prim.mol2 -fo mol2 -c resp -rn
AZA -pf y -at amber*

I have a query can I take the force field parameter for the whole unit in
gaff2 instead of ff14SB.
is it the right thing.
the size of my system is 5 amino acid long wherein N-terminal azobenzene is
connected and C-terminal NH2(NHE) was attached.

Best Regards


On Tue, Sep 1, 2020 at 3:25 AM David A Case <> wrote:

> On Mon, Aug 31, 2020, Aashish Bhatt wrote:
> >
> >I have tried to prepare a force field parameter for azobenzene with
> >conjugated peptide.
> >In the RN=NR bond, antechamber is naming as a dummy(DU) in the mol2 file.
> >As I checked in the parm10.dat file I think the name is N* but I am not
> >sure can you help me with the naming system.
> Can you provide the antechamber command line you are using, along with
> the input PDB file?
> ...thx...dac
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Received on Thu Sep 10 2020 - 04:30:02 PDT
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