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
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> 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
