Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5).

From: Elvis Martis <elvis_bcp.elvismartis.in>
Date: Tue, 25 Aug 2020 14:11:01 +0530

Hi
If the peptide has no unnatural amino acids, the ff14SB force fields
parameters can be applied in leap. Just save the peptide as pdb and treat
as you would treat a protein.

Antechamber step wouldn’t be necessary.

On Tuesday, August 25, 2020, Pooja Kesari <pkesari88.gmail.com> wrote:

> I have a peptide (ESFLE) as substrate for a protein. I have converted this
> file to a mol2 format file using chimera. Now when i am running
> antechamber; it is showing an error message regarding open valency. The C5
> atom belongs to the side chain of glutamic acid.
> Please provide suggestions on how I can overcome this error.
> Is there any other way to add charges to peptide?
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> Thanks & Regards,
> Pooja Kesari
> Post Doctoral Fellow
> Department Of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> INDIA
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
Best Regards
Elvis
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Received on Tue Aug 25 2020 - 02:00:02 PDT
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