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

From: David A Case <>
Date: Tue, 24 Aug 2021 09:13:41 -0400

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.


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Received on Tue Aug 24 2021 - 06:30:02 PDT
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