[gmx-users] D-amino acids' force fields

[Tsjerk Wassenaar]

Hi Mijidorj,

You can see that the modified improper uses the C atom from the previous
residue (-C) in stead of the one of the own residue (C). Whether these
parameters are reliable, I can't tell.

Cheers,

Tsjerk

On Mon, Oct 24, 2016 at 10:04 AM, Mijiddorj Batsaikhan <
b.mijiddorj at gmail.com> wrote:

> Hi Tsjerk,
>
> Thank you for your reply. How can I invert the improper dihedral at the CA?
> I found the D_aminoacids parameters of gromacs which supported by
> SwissParam. I compaired
>
> *ILE’s improper  of Charmm22.ff *
>
>
>
> [ impropers ]
>
> N             C             CA         HN
>
>               C             CA          +N         O
>
> [ cmap ]
>
> -C            N             CA          C             +N
>
>
>
> *DIL’s improper  of SwissParam modified Charmm22.ff *
>
> [ impropers ]
>
>                 N             -C            CA          HN
>
>                 C             CA          +N          O
>
>  [ cmap ]
>
>                 -C            N             CA          C             +N
>
>
>
> How are the swissparam parameters reliable?
>
>
> Best regards,
>
>
> Mijiddorj
>
> ------------------------------
>
> Message: 5
> Date: Sat, 22 Oct 2016 10:11:50 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] D-amino acids' force fields
> Message-ID:
>         <CABzE1Sh3MgjP8puni4mF9sk720JjaAyxaZZGg0W55vHiDaS4sA at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Mijidorj,
>
> These amino acids are chemically and topologically equivalent to their L
> counterparts. For united atom force fields you only need to invert the
> improper dihedral at the C-alpha. For atomistic force fields you don't need
> to change anything, except the CMAP stuff in Charmm for the backbone
> dihedral, and you need to reset the hydrogen position if you used pdb2gmx
> for building the topology and the hydrogens.
>
> Cheers,
>
> Tsjerk
>
> On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" <b.mijiddorj at gmail.com>
> wrote:
>
> > Dear users,
> >
> > Hello, Is there any force field that contains parameters of D-amino
> acids?
> > In my case I need to D-ILE and D-Phe amino acids simulation. Please,
> advice
> > me.
> >
> > Best regards,
> >
> > Mijiddorj
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-- 
Tsjerk A. Wassenaar, Ph.D.