Re: [AMBER] Fwd: leap error for modified amino acid

From: Ipsita Basu <>
Date: Tue, 24 Aug 2021 20:28:26 +0530

Thanks for your reply.
I am using "antechamber -fi pdb -i test_new.pdb -fo ac -o -c bcc -at
amber" and when using gaff for then using gaff instead of amber.
I have used frcmod.cyl as frcmod1.cyl and frcmod2.cyl. I am exactly
following: ""
Actually what I found leap is showing missing bond parameters which should
not be present in the structure.

On Tue, 24 Aug 2021, 18:44 David A Case, <> wrote:

> On Tue, Aug 24, 2021, Ipsita Basu wrote:
> >I am trying to generate parameters for a protein containing modified
> >cysteine residue which I named as "CYL". First I run pdb4amber and
> >then took the output from the non-standard part. It has one nitro
> >group where N is positively charged and one oxygen is negatively
> >charged. If I run antechamber using amber then atomtype is set as "DU"
> >for that oxygen. But using gaff it set all atom types.
> We need more detail here. When you say "run antechamber", what input file
> did you give it, and what command line arguments.
> Similar question: what exactly do you mean by the phrase "using gaff"?
> >run tleap, it is giving error of missing parameters parameters
> It looks like you didn't load the cyl.frcmod file? Was that intentional?
> But it also looks like your atoms types are odd: hx is a hydrogen bonded to
> carbon, but you are missing an os-hx bond parameter. So I think one needs
> to investigate more closely how you obtained your prepin and frcmod files.
> Hence the questions above.
> ....dac
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Received on Tue Aug 24 2021 - 08:00:02 PDT
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