Respected Prof. Case,
Thank you for your suggestion.
With regards,
Saikat
On Mon, May 13, 2019 at 6:22 PM David A Case <david.case.rutgers.edu> wrote:
> On Sun, May 12, 2019, Saikat Dutta chowdhury wrote:
>
> >I am trying to simulate a homopolypeptide in explicit solvent condition.
> >But the amino acid is phosphoglutamate, and I haven't found any parameters
> >for this. Hence I tried antechamber for getting the parameters. I had
> built
> >my polypeptide in Avogadro and followed the "Antechamber Tutorial" to get
> >the parameters.
>
> Antechamber is designed to create parameters for a single residue or
> small molecule, not for polymers. What you want to do is to create a
> single amino acid residue: the general procedure for doing this is
> outlined in the "green fluorescent protein" tutorial. In brief, you
> need to "cap" your desired residue with functional groups, so that you
> have a chemically complete molecule. Then run antechamber, and later
> remove the capping groups.
>
> (I'm cc-ing this to Junmei, since my understanding was that his group had
> simplified procedures for this.)
>
> ...hope this helps...dac
>
>
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--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
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Received on Mon May 13 2019 - 21:30:02 PDT
